Title: | Easy Handling of and Access to Files Organized in Structured Directories |
---|---|
Description: | A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first. |
Authors: | Henrik Bengtsson [aut, cre, cph] |
Maintainer: | Henrik Bengtsson <[email protected]> |
License: | LGPL (>= 2.1) |
Version: | 2.15.1 |
Built: | 2024-08-21 05:15:42 UTC |
Source: | https://github.com/HenrikBengtsson/R.filesets |
A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.
This package should be considered to be in an alpha or beta phase. You should expect the API to be changing over time.
To install this package, call
install.packages("R.filesets")
.
To get started, see:
Please cite references [1] when using this package.
The releases of this package is licensed under LGPL version 2.1 or newer.
The development code of the packages is under a private licence (where applicable) and patches sent to the author fall under the latter license, but will be, if incorporated, released under the "release" license above.
Henrik Bengtsson
[1] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. https://www.r-project.org/conferences/DSC-2003/Proceedings/
Package: R.filesets
Class ChecksumFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ChecksumFile
Directly known subclasses:
public abstract static class ChecksumFile
extends GenericDataFile
A ChecksumFile is an object referring to a file that contains a checksum for a corresponding "main" file.
ChecksumFile(...)
ChecksumFile(...)
... |
Arguments passed to |
Methods:
create |
- | |
getChecksum |
- | |
isOld |
- | |
readChecksum |
Reads the checksum value. | |
validate |
Asserts that the checksum matches the checksum of file. | |
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
Package: R.filesets
Class ChecksumFileSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ChecksumFileSet
Directly known subclasses:
public static class ChecksumFileSet
extends GenericDataFileSet
An ChecksumFileSet object represents a set of ChecksumFile
s.
ChecksumFileSet(...)
ChecksumFileSet(...)
... |
Arguments passed to |
Methods:
readChecksums |
- | |
validate |
- | |
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
Package: R.filesets
Class ColumnNamesInterface
Interface
~~|
~~+--
ColumnNamesInterface
Directly known subclasses:
GenericTabularFile, TabularTextFile
public abstract class ColumnNamesInterface
extends Interface
ColumnNamesInterface(...)
ColumnNamesInterface(...)
... |
Not used. |
Methods:
clearColumnNamesTranslator |
- | |
getColumnNames |
Gets the column names. | |
nbrOfColumns |
Gets the number of columns. | |
setColumnNames |
Sets the column names. | |
setColumnNamesTranslator |
- | |
Methods inherited from Interface:
extend, print, uses
Henrik Bengtsson
Package: R.filesets
Class FullNameInterface
Interface
~~|
~~+--
FullNameInterface
Directly known subclasses:
ChecksumFile, ChecksumFileSet, GenericDataFile, GenericDataFileSet, GenericDataFileSetList, GenericTabularFile, GenericTabularFileSet, RDataFile, RDataFileSet, RdsFile, RdsFileSet, TabularTextFile, TabularTextFileSet
public abstract class FullNameInterface
extends Interface
FullNameInterface(...)
FullNameInterface(...)
... |
Not used. |
The full name consists of a name followed by optional comma-separated tags.
For instance, the full name of foo,a.2,b
has name foo
with
tags a.2
and b
.
Methods:
appendFullNameTranslator |
- | |
clearFullNameTranslator |
- | |
getFullName |
Gets the full name. | |
getName |
Gets the name. | |
getTags |
Gets the tags. | |
hasTag |
- | |
hasTags |
Checks whether the fullname contains a given set of tag(s). | |
setFullName |
Sets the full name. | |
setFullNameTranslator |
- | |
setName |
Sets the name part of the fullname. | |
setTags |
Sets the tags. | |
Methods inherited from Interface:
extend, print, uses
Henrik Bengtsson
# Setup a file set path <- system.file("R", package="R.filesets") ds <- GenericDataFileSet$byPath(path) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Data set # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cat("Path of data set:\n") print(getPath(ds)) cat("Fullname of data set:\n") print(getFullName(ds)) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Data files # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cat("Pathnames:\n") print(getPathnames(ds)) cat("Filenames:\n") print(sapply(ds, getFilename)) cat("Default fullnames:\n") print(getFullNames(ds)) cat("Extensions:\n") print(sapply(ds, getExtension)) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Translation of data file names # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Translate fullnames to lower case setFullNamesTranslator(ds, function(names, ...) tolower(names)) cat("Lower-case fullnames:\n") print(getFullNames(ds)) # Append a translator that reverse the order of the letters revStr <- function(names, ...) { names <- strsplit(names, split="", fixed=TRUE) names <- lapply(names, FUN=rev) names <- sapply(names, FUN=paste, collapse="") names } appendFullNamesTranslator(ds, revStr) cat("Reversed lower-case fullnames:\n") fn3 <- getFullNames(ds) print(fn3) # Alternative for setting up a sequence of translators setFullNamesTranslator(ds, list(function(names, ...) tolower(names), revStr)) cat("Reversed lower-case fullnames:\n") fn3b <- getFullNames(ds) print(fn3b) stopifnot(identical(fn3b, fn3)) # Reset clearFullNamesTranslator(ds) cat("Default fullnames (after resetting):\n") print(getFullNames(ds))
# Setup a file set path <- system.file("R", package="R.filesets") ds <- GenericDataFileSet$byPath(path) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Data set # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cat("Path of data set:\n") print(getPath(ds)) cat("Fullname of data set:\n") print(getFullName(ds)) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Data files # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cat("Pathnames:\n") print(getPathnames(ds)) cat("Filenames:\n") print(sapply(ds, getFilename)) cat("Default fullnames:\n") print(getFullNames(ds)) cat("Extensions:\n") print(sapply(ds, getExtension)) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Translation of data file names # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Translate fullnames to lower case setFullNamesTranslator(ds, function(names, ...) tolower(names)) cat("Lower-case fullnames:\n") print(getFullNames(ds)) # Append a translator that reverse the order of the letters revStr <- function(names, ...) { names <- strsplit(names, split="", fixed=TRUE) names <- lapply(names, FUN=rev) names <- sapply(names, FUN=paste, collapse="") names } appendFullNamesTranslator(ds, revStr) cat("Reversed lower-case fullnames:\n") fn3 <- getFullNames(ds) print(fn3) # Alternative for setting up a sequence of translators setFullNamesTranslator(ds, list(function(names, ...) tolower(names), revStr)) cat("Reversed lower-case fullnames:\n") fn3b <- getFullNames(ds) print(fn3b) stopifnot(identical(fn3b, fn3)) # Reset clearFullNamesTranslator(ds) cat("Default fullnames (after resetting):\n") print(getFullNames(ds))
Package: R.filesets
Class GenericDataFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
Directly known subclasses:
ChecksumFile, GenericTabularFile, RDataFile, RdsFile, TabularTextFile
public abstract static class GenericDataFile
extends FullNameInterface
A GenericDataFile is an object referring to a data file on a file system.
Note that this class is abstract and can not be instantiated, but
instead you have to use one of the subclasses or the generic
*fromFile()
method.
GenericDataFile(filename=NULL, path=NULL, mustExist=!is.na(filename), ..., .onUnknownArgs=c("error", "warning", "ignore"))
GenericDataFile(filename=NULL, path=NULL, mustExist=!is.na(filename), ..., .onUnknownArgs=c("error", "warning", "ignore"))
filename |
The filename of the file. |
path |
An optional path to the file. |
mustExist |
If |
... |
Not used. |
.onUnknownArgs |
A |
Methods:
compareChecksum |
Compares the file checksum with the value of the checksum file. | |
equals |
Checks if a file equals another. | |
getChecksum |
Gets the checksum of a file. | |
getChecksumFile |
- | |
getExtension |
Gets the filename extension. | |
getFileSize |
Gets the size of a file. | |
getFileType |
Gets the file type of a file. | |
getFilename |
Gets the filename of the file. | |
getPath |
Gets the path (directory) of the file. | |
getPathname |
Gets the pathname of the file. | |
is.na |
- | |
isFile |
Checks if this is an existing file. | |
validateChecksum |
Asserts that the file checksum matches the one of the checksum file. | |
writeChecksum |
Write the file checksum to a checksum file. | |
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
The filename of an GenericDataFile
is structured as follows:
: "sample001,a,b,c.CEL"
(this follows the R convention, but not the Unix convention)
: "sample001,a,b,c"
: "sample001"
: c("a", "b", "c")
: "CEL"
Henrik Bengtsson
An object of this class is typically part of an GenericDataFileSet
.
Package: R.filesets
Class GenericDataFileSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
Directly known subclasses:
ChecksumFileSet, GenericTabularFileSet, RDataFileSet, RdsFileSet, TabularTextFileSet
public static class GenericDataFileSet
extends FullNameInterface
A GenericDataFileSet object represents a set of GenericDataFile
s.
GenericDataFileSet(files=NULL, tags="*", depth=NULL, ..., .onUnknownArgs=c("error", "warning", "ignore"))
GenericDataFileSet(files=NULL, tags="*", depth=NULL, ..., .onUnknownArgs=c("error", "warning", "ignore"))
files |
A |
tags |
A |
depth |
An non-negative |
... |
Not used. |
.onUnknownArgs |
A |
Methods:
anyDuplicated |
- | |
anyNA |
- | |
append |
- | |
appendFiles |
- | |
as.list |
- | |
byName |
- | |
byPath |
- | |
duplicated |
- | |
equals |
- | |
extract |
- | |
getChecksum |
- | |
getChecksumFileSet |
- | |
getDefaultFullName |
- | |
getFile |
- | |
getFileClass |
- | |
getFileSize |
- | |
getFullNames |
- | |
getNames |
- | |
getOneFile |
- | |
getPath |
- | |
getPathnames |
- | |
gunzip |
- | |
gzip |
- | |
hasFile |
- | |
indexOf |
- | |
is.na |
- | |
sortBy |
- | |
unique |
- | |
validate |
- | |
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
# Setup a file set path <- system.file(package="R.filesets") ds <- GenericDataFileSet$byPath(path) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Data set # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cat("Path of data set:\n") print(getPath(ds)) cat("Fullname of data set:\n") print(getFullName(ds)) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Data files # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cat("Pathnames:\n") print(getPathnames(ds)) cat("Filenames:\n") print(sapply(ds, getFilename)) cat("Extensions:\n") print(sapply(ds, getExtension)) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Subsetting # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - n <- length(ds) ds2 <- extract(ds, 1:n) print(ds2) ds3 <- extract(ds, n:1) print(ds3) stopifnot(identical(rev(getPathnames(ds3)), getPathnames(ds2))) idxs <- c(1,2,NA,n,NA) ds4 <- extract(ds, idxs, onMissing="NA") print(ds4) print(getFullNames(ds4)) print(getFiles(ds4)) stopifnot(identical(is.na(idxs), unname(is.na(getPathnames(ds4)))))
# Setup a file set path <- system.file(package="R.filesets") ds <- GenericDataFileSet$byPath(path) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Data set # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cat("Path of data set:\n") print(getPath(ds)) cat("Fullname of data set:\n") print(getFullName(ds)) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Data files # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cat("Pathnames:\n") print(getPathnames(ds)) cat("Filenames:\n") print(sapply(ds, getFilename)) cat("Extensions:\n") print(sapply(ds, getExtension)) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Subsetting # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - n <- length(ds) ds2 <- extract(ds, 1:n) print(ds2) ds3 <- extract(ds, n:1) print(ds3) stopifnot(identical(rev(getPathnames(ds3)), getPathnames(ds2))) idxs <- c(1,2,NA,n,NA) ds4 <- extract(ds, idxs, onMissing="NA") print(ds4) print(getFullNames(ds4)) print(getFiles(ds4)) stopifnot(identical(is.na(idxs), unname(is.na(getPathnames(ds4)))))
Package: R.filesets
Class GenericDataFileSetList
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSetList
Directly known subclasses:
public static class GenericDataFileSetList
extends FullNameInterface
A GenericDataFileSetList object represents a list of
GenericDataFileSet
s.
GenericDataFileSetList(dsList=list(), tags="*", ..., allowDuplicates=TRUE, .setClass="GenericDataFileSet")
GenericDataFileSetList(dsList=list(), tags="*", ..., allowDuplicates=TRUE, .setClass="GenericDataFileSet")
dsList |
A single or a |
tags |
|
... |
Not used. |
allowDuplicates |
If |
.setClass |
A |
Methods:
as |
- | |
as.GenericDataFileSetList |
- | |
as.list |
- | |
getFileList |
- | |
getFullNames |
- | |
getNames |
- | |
getSet |
- | |
getSets |
- | |
indexOf |
- | |
length |
- | |
nbrOfSets |
- | |
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
# Setup a file set path1 <- system.file(package="R.filesets") ds1 <- GenericDataFileSet$byPath(path1) path2 <- system.file(package="R.utils") ds2 <- GenericDataFileSet$byPath(path2) dsl <- GenericDataFileSetList(list(ds1, ds2), tags=c("*", "CustomTag")) print(dsl) df <- as.data.frame(dsl) print(df) print(df["DESCRIPTION","R.filesets"])
# Setup a file set path1 <- system.file(package="R.filesets") ds1 <- GenericDataFileSet$byPath(path1) path2 <- system.file(package="R.utils") ds2 <- GenericDataFileSet$byPath(path2) dsl <- GenericDataFileSetList(list(ds1, ds2), tags=c("*", "CustomTag")) print(dsl) df <- as.data.frame(dsl) print(df) print(df["DESCRIPTION","R.filesets"])
Package: R.filesets
Class GenericTabularFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
Directly known subclasses:
TabularTextFile
public abstract static class GenericTabularFile
extends ColumnNamesInterface
A TabularTextFile is an object referring to a tabular text file on a file system containing data in a tabular format. Methods for reading all or a subset of the tabular data exist.
GenericTabularFile(..., .verify=TRUE, verbose=FALSE)
GenericTabularFile(..., .verify=TRUE, verbose=FALSE)
... |
Arguments passed to |
.verify , verbose
|
(Internal only) If |
Methods:
dim |
- | |
extractMatrix |
- | |
head |
- | |
nbrOfColumns |
- | |
nbrOfRows |
- | |
readColumns |
- | |
readDataFrame |
- | |
tail |
- | |
writeColumnsToFiles |
- | |
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
An object of this class is typically part of an
GenericTabularFileSet
.
Package: R.filesets
Class GenericTabularFileSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
Directly known subclasses:
TabularTextFileSet
public static class GenericTabularFileSet
extends GenericDataFileSet
An GenericTabularFileSet object represents a set of
GenericTabularFile
s.
GenericTabularFileSet(...)
GenericTabularFileSet(...)
... |
Arguments passed to |
Methods:
extractMatrix |
- | |
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
Reads data from a RDS file.
## Default S3 method: loadRDS(file, ...) ## S3 method for class 'RdsFile' loadRDS(file, ...)
## Default S3 method: loadRDS(file, ...) ## S3 method for class 'RdsFile' loadRDS(file, ...)
file |
A |
... |
Additional arguments passed to |
Returns an R object.
Henrik Bengtsson
readRDS
().
Reads data from a RDS file.
## S3 method for class 'RDataFile' loadToEnv(file, ...)
## S3 method for class 'RDataFile' loadToEnv(file, ...)
file |
A |
... |
Additional arguments passed to |
Returns an environment
.
Henrik Bengtsson
Package: R.filesets
Class RDataFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RDataFile
Directly known subclasses:
public abstract static class RDataFile
extends GenericDataFile
An RDataFile represents a binary file containing R objects
saved using the save
() function.
RDataFile(...)
RDataFile(...)
... |
Arguments passed to |
Methods:
loadObject |
- | |
loadToEnv |
- | |
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
An object of this class is typically part of an RDataFileSet
.
Package: R.filesets
Class RDataFileSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RDataFileSet
Directly known subclasses:
public static class RDataFileSet
extends GenericDataFileSet
An RDataFileSet object represents a set of RDataFile
:s.
RDataFileSet(...)
RDataFileSet(...)
... |
Arguments passed to |
Methods:
byPath |
- | |
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
Package: R.filesets
Class RdsFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RdsFile
Directly known subclasses:
public abstract static class RdsFile
extends GenericDataFile
An RdsFile represents a binary file containing an R object
saved using the saveRDS
() function.
RdsFile(...)
RdsFile(...)
... |
Arguments passed to |
Methods:
loadObject |
- | |
loadRDS |
- | |
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
An object of this class is typically part of an RdsFileSet
.
Package: R.filesets
Class RdsFileSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
RdsFileSet
Directly known subclasses:
public static class RdsFileSet
extends GenericDataFileSet
An RdsFileSet object represents a set of RdsFile
:s.
RdsFileSet(...)
RdsFileSet(...)
... |
Arguments passed to |
Methods:
byPath |
- | |
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
Reads data from a tabular file or a set of such files.
## Default S3 method: readDataFrame(filename, path=NULL, ...)
## Default S3 method: readDataFrame(filename, path=NULL, ...)
filename , path
|
|
... |
Additional arguments passed to either
(i) |
When reading multiple files at once, first each file is read into
a data.frame
, and then these data.frame
s are (by default) merged into
one data.frame
using rbind
(). This requires that the
same set of columns are read for each file. Which columns to read
can be controlled by specifying their names in
argument colClasses
. To change how the data.frame
s are
merged, use argument combineBy
.
For more information, follow the help on the above to
readDataFrame()
help links.
Returns a data.frame
.
Henrik Bengtsson
read.table
.
For further details, see classes TabularTextFile
and
TabularTextFileSet
.
path <- system.file("exData/dataSetA,original", package="R.filesets") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Example: Standard tab-delimited file with header comments # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pathname <- file.path(path, "fileA,20100112.dat") # Read all data df <- readDataFrame(pathname) print(df) # Read columns 'x', 'y', and 'char' df <- readDataFrame(pathname, colClasses=c("(x|y)"="integer", "char"="character")) print(df) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Example: Tab-delimited file with header comments but # also two garbage at the very beginning # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pathname <- file.path(path, "fileA,20130116.datx") # Explicitly skip the two rows df <- readDataFrame(pathname, skip=2) print(df) # Skip until the first data row df <- readDataFrame(pathname, skip="^x") print(df) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Example: Tab-delimited file without column header # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - path <- system.file("exData/dataSetB", package="R.filesets") pathname <- file.path(path, "fileF,noHeader.dat") # Incorrectly assuming column header df <- readDataFrame(pathname) print(df) # No column header df <- readDataFrame(pathname, header=FALSE) print(df)
path <- system.file("exData/dataSetA,original", package="R.filesets") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Example: Standard tab-delimited file with header comments # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pathname <- file.path(path, "fileA,20100112.dat") # Read all data df <- readDataFrame(pathname) print(df) # Read columns 'x', 'y', and 'char' df <- readDataFrame(pathname, colClasses=c("(x|y)"="integer", "char"="character")) print(df) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Example: Tab-delimited file with header comments but # also two garbage at the very beginning # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pathname <- file.path(path, "fileA,20130116.datx") # Explicitly skip the two rows df <- readDataFrame(pathname, skip=2) print(df) # Skip until the first data row df <- readDataFrame(pathname, skip="^x") print(df) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Example: Tab-delimited file without column header # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - path <- system.file("exData/dataSetB", package="R.filesets") pathname <- file.path(path, "fileF,noHeader.dat") # Incorrectly assuming column header df <- readDataFrame(pathname) print(df) # No column header df <- readDataFrame(pathname, header=FALSE) print(df)
Package: R.filesets
Class TabularTextFile
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFile
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
ColumnNamesInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
GenericTabularFile
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
TabularTextFile
Directly known subclasses:
public abstract static class TabularTextFile
extends GenericTabularFile
A TabularTextFile is an object referring to a tabular text file on a file system containing data in a tabular format. Methods for reading all or a subset of the tabular data exist.
TabularTextFile(..., sep=c("\t", ","), quote="\"", fill=FALSE, skip=0L, columnNames=NA, commentChar="#", .verify=TRUE, verbose=FALSE)
TabularTextFile(..., sep=c("\t", ","), quote="\"", fill=FALSE, skip=0L, columnNames=NA, commentChar="#", .verify=TRUE, verbose=FALSE)
... |
Arguments passed to |
sep |
A |
quote |
A |
fill |
As in |
skip |
As in |
columnNames |
A |
commentChar |
A single |
.verify , verbose
|
(Internal only) If |
Methods:
getHeader |
- | |
nbrOfLines |
- | |
nbrOfRows |
- | |
readDataFrame |
- | |
readLines |
- | |
Methods inherited from GenericTabularFile:
[, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles
Methods inherited from ColumnNamesInterface:
appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames
Methods inherited from GenericDataFile:
as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
An object of this class is typically part of an TabularTextFileSet
.
path <- system.file("exData/dataSetA,original", package="R.filesets") db <- TabularTextFile("fileA,20100112.dat", path=path) print(db) # Read all data data <- readDataFrame(db) print(data) # Read columns 'x', 'y', and 'char' data <- readDataFrame(db, colClasses=c("(x|y)"="integer", "char"="character")) print(data) # Translate column names on the fly db <- setColumnNamesTranslator(db, function(names, ...) toupper(names)) data <- readDataFrame(db, colClasses=c("(X|Y)"="integer", "CHAR"="character")) print(data)
path <- system.file("exData/dataSetA,original", package="R.filesets") db <- TabularTextFile("fileA,20100112.dat", path=path) print(db) # Read all data data <- readDataFrame(db) print(data) # Read columns 'x', 'y', and 'char' data <- readDataFrame(db, colClasses=c("(x|y)"="integer", "char"="character")) print(data) # Translate column names on the fly db <- setColumnNamesTranslator(db, function(names, ...) toupper(names)) data <- readDataFrame(db, colClasses=c("(X|Y)"="integer", "CHAR"="character")) print(data)
Package: R.filesets
Class TabularTextFileSet
Object
~~|
~~+--
FullNameInterface
~~~~~~~|
~~~~~~~+--
GenericDataFileSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
GenericTabularFileSet
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
TabularTextFileSet
Directly known subclasses:
public static class TabularTextFileSet
extends GenericTabularFileSet
An TabularTextFileSet object represents a set of TabularTextFile
s.
TabularTextFileSet(...)
TabularTextFileSet(...)
... |
Arguments passed to |
Methods:
readDataFrame |
- | |
Methods inherited from GenericTabularFileSet:
extractMatrix
Methods inherited from GenericDataFileSet:
[, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate
Methods inherited from FullNameInterface:
appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save
Henrik Bengtsson
# Setup a file set consisting of all *.dat tab-delimited files # in a particular directory path <- system.file("exData/dataSetA,original", package="R.filesets") ds <- TabularTextFileSet$byPath(path, pattern="[.]dat$") print(ds) # Read column 'y' and a subset of the rows from each of the # tab-delimited files and combine into a matrix rows <- c(3:5, 8, 2) data <- extractMatrix(ds, column="y", colClass="integer", rows=rows) print(data) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # See also help("readDataFrame.TabularTextFileSet") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ADVANCED: Translation of fullnames # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fnts <- TabularTextFileSet$byPath(getPath(ds), pattern=",fullnames[.]txt$") appendFullNamesTranslator(ds, as.list(fnts)) cat("Default fullnames:\n") print(head(getFullNames(ds, translate=FALSE))) cat("Translated fullnames:\n") print(head(getFullNames(ds))) cat("Default fullnames:\n") print(getFullNames(ds, translate=FALSE)) cat("Translated fullnames:\n") print(getFullNames(ds))
# Setup a file set consisting of all *.dat tab-delimited files # in a particular directory path <- system.file("exData/dataSetA,original", package="R.filesets") ds <- TabularTextFileSet$byPath(path, pattern="[.]dat$") print(ds) # Read column 'y' and a subset of the rows from each of the # tab-delimited files and combine into a matrix rows <- c(3:5, 8, 2) data <- extractMatrix(ds, column="y", colClass="integer", rows=rows) print(data) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # See also help("readDataFrame.TabularTextFileSet") # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # ADVANCED: Translation of fullnames # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fnts <- TabularTextFileSet$byPath(getPath(ds), pattern=",fullnames[.]txt$") appendFullNamesTranslator(ds, as.list(fnts)) cat("Default fullnames:\n") print(head(getFullNames(ds, translate=FALSE))) cat("Translated fullnames:\n") print(head(getFullNames(ds))) cat("Default fullnames:\n") print(getFullNames(ds, translate=FALSE)) cat("Translated fullnames:\n") print(getFullNames(ds))