Title: | Copy-Number Analysis of Large Microarray Data Sets |
---|---|
Description: | Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data. |
Authors: | Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut] |
Maintainer: | Henrik Bengtsson <[email protected]> |
License: | LGPL (>= 2.1) |
Version: | 1.7.1 |
Built: | 2024-08-15 04:07:00 UTC |
Source: | https://github.com/HenrikBengtsson/aroma.cn |
Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.
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("aroma.cn")
.
To get started, see:
...
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, Pierre Neuvial
Please cite PSCBS using one or more of the following references:
A.B. Olshen, H. Bengtsson, P. Neuvial, P.T. Spellman, R.A. Olshen, V.E. Seshan. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation, Bioinformatics, 2011
Please cite PSCBS using one or more of the following references:
H. Bengtsson, P. Neuvial and T.P. Speed. TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays, BMC Bioinformatics, 2010
H. Bengtsson, A. Ray, P. Spellman and T.P. Speed. A single-sample method for normalizing and combining full-resolutioncopy numbers from multiple platforms, labs and analysis methods, Bioinformatics, 2009
H. Bengtsson; K. Simpson; J. Bullard; K. Hansen. aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report 745, Department of Statistics, University of California, Berkeley, February 2008
H. Bengtsson, R. Irizarry, B. Carvalho, & T.P. Speed. Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics, 2008
To see these entries in BibTeX format, use 'print(<citation>, bibtex=TRUE)', 'toBibtex(.)', or set 'options(citation.bibtex.max=999)'.
Package: aroma.cn
Class AbstractCurveNormalization
Object
~~|
~~+--
AbstractCurveNormalization
Directly known subclasses:
PrincipalCurveNormalization, XYCurveNormalization
public abstract static class AbstractCurveNormalization
extends Object
AbstractCurveNormalization(dataSet=NULL, targetSet=NULL, subsetToFit=NULL, tags="*", copyTarget=TRUE, ...)
AbstractCurveNormalization(dataSet=NULL, targetSet=NULL, subsetToFit=NULL, tags="*", copyTarget=TRUE, ...)
dataSet |
An |
targetSet |
An |
subsetToFit |
The subset of loci to be used to fit the
normalization functions.
If |
tags |
(Optional) Sets the tags for the output data sets. |
copyTarget |
If |
... |
Not used. |
Methods:
getFullName |
- | |
getInputDataSet |
- | |
getName |
- | |
getOutputDataSet |
- | |
getTags |
- | |
getTargetDataSet |
- | |
process |
- | |
setTags |
- | |
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, asThis
Henrik Bengtsson
Calls XX or XY from ChrX allele B fractions of a normal sample.
## S3 method for class 'numeric' callXXorXY(betaX, betaY=NULL, flavor=c("density"), adjust=1.5, ..., censorAt=c(-0.5, +1.5), verbose=FALSE)
## S3 method for class 'numeric' callXXorXY(betaX, betaY=NULL, flavor=c("density"), adjust=1.5, ..., censorAt=c(-0.5, +1.5), verbose=FALSE)
betaX |
|
betaY |
A optional |
flavor |
A |
adjust |
A postive |
... |
Additional arguments passed to
|
censorAt |
A |
verbose |
Returns a ...
Missing and non-finite values are dropped before trying to call XX or XY.
Henrik Bengtsson, Pierre Neuvial
Internally findPeaksAndValleys
is used to identify
the thresholds.
Package: aroma.cn
Class MultiSourceCopyNumberNormalization
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
MultiSourceCopyNumberNormalization
Directly known subclasses:
public static class MultiSourceCopyNumberNormalization
extends ParametersInterface
The multi-source copy-number normalization (MSCN) method [1] is a normalization method that normalizes copy-number estimates measured by multiple sites and/or platforms for common samples. It normalizes the estimates toward a common scale such that for any copy-number level the mean level of the normalized data are the same.
MultiSourceCopyNumberNormalization(dsList=NULL, fitUgp=NULL, subsetToFit=NULL, targetDimension=1, align=c("byChromosome", "none"), tags="*", ...)
MultiSourceCopyNumberNormalization(dsList=NULL, fitUgp=NULL, subsetToFit=NULL, targetDimension=1, align=c("byChromosome", "none"), tags="*", ...)
dsList |
A |
fitUgp |
An |
subsetToFit |
The subset of loci (as mapped by the |
targetDimension |
A |
align |
A |
tags |
(Optional) Sets the tags for the output data sets. |
... |
Not used. |
The multi-source normalization method is by nature a single-sample method, that is, it normalizes arrays for one sample at the time and independently of all other samples/arrays.
However, the current implementation is such that it first generates smoothed data for all samples/arrays. Then, it normalizes the sample one by one.
Methods:
getAllNames |
- | |
getAsteriskTags |
- | |
getInputDataSets |
- | |
getOutputDataSets |
- | |
getTags |
- | |
nbrOfDataSets |
- | |
process |
- | |
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
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, asThis
Some preprocessing methods estimate copy numbers on sex chromosomes differently from the autosomal chromosomes. The way this is done may vary from method to method and we cannot assume anything about what approach is. This is the main reason why the estimation of the normalization function is by default based on signals from autosomal chromosomes only; this protects the estimate of the function from being biased by specially estimated sex-chromosome signals. Note that the normalization function is still applied to all chromosomes.
This means that if the transformation applied by a particular preprocessing method is not the same for the sex chromosomes as the autosomal chromosomes, the normalization applied on the sex chromosomes is not optimal one. This is why multi-source normalization sometimes fails to bring sex-chromosome signals to the same scale across sources. Unfortunately, there is no automatic way to handle this. The only way would be to fit a specific normalization function to each of the sex chromosomes, but that would require that there exist copy-number abberations on those chromosomes, which could be a too strong assumption.
A more conservative approach is to normalize the signals such that
afterward the median of the smoothed copy-number levels are the same
across sources for any particular chromosome.
This is done by setting argument align="byChromosome"
.
Henrik Bengtsson
[1] H. Bengtsson, A. Ray, P. Spellman & T.P. Speed,
A single-sample method for normalizing and combining
full-resolution copy numbers from multiple platforms,
labs and analysis methods,
Bioinformatics 2009.
Package: aroma.cn
Class PairedPscbsModel
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
PairedPscbsModel
Directly known subclasses:
public static class PairedPscbsModel
extends ParametersInterface
This class represents the Paired PSCBS method [1], which segments matched tumor-normal parental copy-number data into piecewise constant segments.
PairedPscbsModel(dsT=NULL, dsN=NULL, tags="*", ..., dropTcnOutliers=TRUE, gapMinLength=1e+06, seed=NULL)
PairedPscbsModel(dsT=NULL, dsN=NULL, tags="*", ..., dropTcnOutliers=TRUE, gapMinLength=1e+06, seed=NULL)
dsT , dsN
|
The tumor and the normal
|
tags |
Tags added to the output data sets. |
... |
(Optional) Additional arguments passed to
|
dropTcnOutliers |
If |
gapMinLength |
Genomic regions with no data points that are of
this length and greater are considered to be "gaps" and are ignored
in the segmentation. If + |
seed |
An optional |
Methods:
fit |
- | |
getChipType |
- | |
getChromosomes |
- | |
getDataSets |
- | |
getFullName |
- | |
getName |
- | |
getNormalDataSet |
- | |
getOutputDataSet |
- | |
getTags |
- | |
getTumorDataSet |
- | |
indexOf |
- | |
nbrOfFiles |
- | |
setTags |
- | |
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
[1] ...
...
## Not run: dataSet <- "GSE12702" tags <- "ASCRMAv2" chipType <- "Mapping250K_Nsp" ds <- AromaUnitPscnBinarySet$byName(dataSet, tags=tags, chipType=chipType) print(ds) # Extract tumors and normals idxs <- seq(from=1, to=nbrOfFiles(ds), by=2) dsT <- extract(ds, idxs); idxs <- seq(from=2, to=nbrOfFiles(ds), by=2) dsN <- extract(ds, idxs); # Setup Paired PSCBS model seg <- PairedPscbsModel(dsT=dsT, dsN=dsN) print(seg) # Segment all tumor-normal pairs fit(seg, verbose=-10) ## End(Not run)
## Not run: dataSet <- "GSE12702" tags <- "ASCRMAv2" chipType <- "Mapping250K_Nsp" ds <- AromaUnitPscnBinarySet$byName(dataSet, tags=tags, chipType=chipType) print(ds) # Extract tumors and normals idxs <- seq(from=1, to=nbrOfFiles(ds), by=2) dsT <- extract(ds, idxs); idxs <- seq(from=2, to=nbrOfFiles(ds), by=2) dsN <- extract(ds, idxs); # Setup Paired PSCBS model seg <- PairedPscbsModel(dsT=dsT, dsN=dsN) print(seg) # Segment all tumor-normal pairs fit(seg, verbose=-10) ## End(Not run)
Package: aroma.cn
Class PrincipalCurveNormalization
Object
~~|
~~+--
AbstractCurveNormalization
~~~~~~~|
~~~~~~~+--
PrincipalCurveNormalization
Directly known subclasses:
public static class PrincipalCurveNormalization
extends AbstractCurveNormalization
PrincipalCurveNormalization(..., subset=1/20)
PrincipalCurveNormalization(..., subset=1/20)
... |
Arguments passed to |
subset |
A |
Methods:
No methods defined.
Methods inherited from AbstractCurveNormalization:
as.character, backtransformOne, fitOne, getAsteriskTags, getDataSets, getFullName, getInputDataSet, getName, getOutputDataSet, getPairedDataSet, getPath, getRootPath, getSubsetToFit, getTags, getTargetDataSet, nbrOfFiles, process, setTags
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, asThis
Henrik Bengtsson
Package: aroma.cn
Class TotalCnBinnedSmoothing
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
TotalCnSmoothing
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
TotalCnBinnedSmoothing
Directly known subclasses:
public static class TotalCnBinnedSmoothing
extends TotalCnSmoothing
TotalCnBinnedSmoothing(..., robust=FALSE)
TotalCnBinnedSmoothing(..., robust=FALSE)
... |
Arguments passed to |
robust |
If |
Note that dsS <- TotalCnBinnedSmoothing(ds, targetUgp=ugp)
where
ugp <- getAromaUgpFile(ds)
returns a data set with an identical
set of loci as the input data set and identical signals as the
input ones, except for loci with duplicated positions. If all
loci have unique positions, the the output is identical to the input.
Methods:
No methods defined.
Methods inherited from TotalCnSmoothing:
getAsteriskTags, getOutputDataSet0, getOutputFileClass, getOutputFileExtension, getOutputFileSetClass, getOutputFiles, getParameters, getPath, getRootPath, getTargetPositions, getTargetUgpFile, process, smoothRawCopyNumbers
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
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, asThis
Henrik Bengtsson
Package: aroma.cn
Class TotalCnKernelSmoothing
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
TotalCnSmoothing
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
TotalCnKernelSmoothing
Directly known subclasses:
public static class TotalCnKernelSmoothing
extends TotalCnSmoothing
TotalCnKernelSmoothing(..., kernel=c("gaussian", "uniform"), bandwidth=50000, censorH=3, robust=FALSE)
TotalCnKernelSmoothing(..., kernel=c("gaussian", "uniform"), bandwidth=50000, censorH=3, robust=FALSE)
... |
Arguments passed to |
kernel |
A |
bandwidth |
A |
censorH |
A positive |
robust |
If |
Methods:
No methods defined.
Methods inherited from TotalCnSmoothing:
getAsteriskTags, getOutputDataSet0, getOutputFileClass, getOutputFileExtension, getOutputFileSetClass, getOutputFiles, getParameters, getPath, getRootPath, getTargetPositions, getTargetUgpFile, process, smoothRawCopyNumbers
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
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, asThis
Henrik Bengtsson
Package: aroma.cn
Class TotalCnSmoothing
Object
~~|
~~+--
ParametersInterface
~~~~~~~|
~~~~~~~+--
AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
TotalCnSmoothing
Directly known subclasses:
TotalCnBinnedSmoothing, TotalCnKernelSmoothing
public abstract static class TotalCnSmoothing
extends AromaTransform
TotalCnSmoothing(dataSet=NULL, ..., targetUgp=NULL, .reqSetClass="AromaUnitTotalCnBinarySet")
TotalCnSmoothing(dataSet=NULL, ..., targetUgp=NULL, .reqSetClass="AromaUnitTotalCnBinarySet")
dataSet |
|
... |
Arguments passed to |
targetUgp |
An |
.reqSetClass |
(internal only) |
Methods:
getTargetUgpFile |
- | |
process |
- | |
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
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, asThis
Henrik Bengtsson
Package: aroma.cn
Class TumorBoostNormalization
Object
~~|
~~+--
TumorBoostNormalization
Directly known subclasses:
public static class TumorBoostNormalization
extends Object
TumorBoost is normalization method that normalizes the allele B fractions of a tumor sample given the allele B fractions and genotype calls for a matched normal. The method is a single-sample (single-pair) method. It does not require total copy number estimates. The normalization is done such that the total copy number is unchanged afterwards.
TumorBoostNormalization(dsT=NULL, dsN=NULL, gcN=NULL, flavor=c("v4", "v3", "v2", "v1"), preserveScale=TRUE, collapseHomozygous=FALSE, tags="*", ...)
TumorBoostNormalization(dsT=NULL, dsN=NULL, gcN=NULL, flavor=c("v4", "v3", "v2", "v1"), preserveScale=TRUE, collapseHomozygous=FALSE, tags="*", ...)
dsT |
An |
dsN |
An |
gcN |
An |
flavor |
A |
preserveScale |
If |
collapseHomozygous |
If |
tags |
(Optional) Sets the tags for the output data sets. |
... |
Not used. |
Methods:
getFullName |
- | |
getInputDataSet |
- | |
getName |
- | |
getNormalDataSet |
- | |
getNormalGenotypeCallSet |
- | |
getOutputDataSet |
- | |
getTags |
- | |
nbrOfFiles |
- | |
process |
- | |
setTags |
- | |
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, asThis
Henrik Bengtsson, Pierre Neuvial
Package: aroma.cn
Class XYCurveNormalization
Object
~~|
~~+--
AbstractCurveNormalization
~~~~~~~|
~~~~~~~+--
XYCurveNormalization
Directly known subclasses:
public static class XYCurveNormalization
extends AbstractCurveNormalization
XYCurveNormalization(...)
XYCurveNormalization(...)
... |
Arguments passed to |
Methods:
No methods defined.
Methods inherited from AbstractCurveNormalization:
as.character, backtransformOne, fitOne, getAsteriskTags, getDataSets, getFullName, getInputDataSet, getName, getOutputDataSet, getPairedDataSet, getPath, getRootPath, getSubsetToFit, getTags, getTargetDataSet, nbrOfFiles, process, setTags
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, asThis
Henrik Bengtsson