Provides classes similar to ExpressionSet for copy number analysis


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Documentation for package ‘genoset’ version 1.16.2

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genoset-package GenoSet: An eSet for data with genome locations
baf2mbaf Calculate mBAF from BAF
boundingIndices Find indices of features bounding a set of chromosome ranges/genes
boundingIndices2 Find indices of features bounding a set of chromosome ranges/genes
boundingIndicesByChr Find indices of features bounding a set of chromosome ranges/genes, across chromosomes
bounds2Rle Convert bounding indices into a Rle
calcGC Calculate GC Percentage in windows
chr Chromosome name for each feature
chr-method Chromosome name for each feature
chrIndices Get a matrix of first and last index of features in each chromosome
chrIndices-method Get a matrix of first and last index of features in each chromosome
chrInfo Get chromosome start and stop positions
chrInfo-method Get chromosome start and stop positions
chrNames Get list of unique chromosome names
chrNames-method Get list of unique chromosome names
chrNames<- Get list of unique chromosome names
chrNames<--method Get list of unique chromosome names
chrOrder Order chromosome names in proper genome order
cn2lr Take vector or matrix of copynumber values, convert to log2ratios
cn2lr-method Take vector or matrix of copynumber values, convert to log2ratios
colMeans Means of columns
colMeans-method Means of columns
colnames-method Get colnames from a GenoSet
colnames<--method Get colnames from a GenoSet
dim-method Dimensions
elementLengths-method Get elementLengths from locData slot
end-method Get end of location for each feature
fake.baf Example GenoSet, BAFSet, and CNSet objects and the data to create them.
fake.cn Example GenoSet, BAFSet, and CNSet objects and the data to create them.
fake.lrr Example GenoSet, BAFSet, and CNSet objects and the data to create them.
fake.pData Example GenoSet, BAFSet, and CNSet objects and the data to create them.
featureNames-method Get rownames from GRanges, or GenoSet
featureNames<--method Get rownames from GRanges, or GenoSet
fixSegNAs Fix NA runs in a Rle
gcCorrect Correct copy number for GC content
genome Get and set the genome universe annotation.
genome-method Genome version
genomeAxis Label axis with base pair units
genoPlot Plot data along the genome
genoPlot-method Plot data along the genome
genoPos Get base positions of features in genome-scale units
genoPos-method Get base positions of features in genome-scale units
GenoSet Create a GenoSet object
genoset GenoSet: An eSet for data with genome locations
GenoSet-class Class '"GenoSet"'
genoset-datasets Example GenoSet, BAFSet, and CNSet objects and the data to create them.
genoset-defunct Defunct genoset features
genoset-deprecated Deprecated genoset features
genoset.ds Example GenoSet, BAFSet, and CNSet objects and the data to create them.
GenoSetOrGenomicRanges-class Class '"GenoSet"'
initGenoSet Create a GenoSet or derivative object
isGenomeOrder Check if a GRanges orGenoSet is in genome order
isGenomeOrder-method Check if a GRanges orGenoSet is in genome order
locData Access the feature genome position info
locData-method Access the feature genome position info
locData.gr Example GenoSet, BAFSet, and CNSet objects and the data to create them.
locData<- Access the feature genome position info
locData<--method Access the feature genome position info
lr2cn Take vector or matrix of log2 ratios, convert to copynumber
modeCenter Center continuous data on mode
names-method Get data matrix names
nrow-method Number of rows
pos Chromosome position of features
pos-method Chromosome position of features
rangeColMeans Calculate column means for multiple ranges
RangedDataOrGenomicRanges-class Class '"GenoSet"'
RangedDataOrGenoset-class Class '"GenoSet"'
RangedDataOrGenoSetOrGenomicRanges-class Class '"GenoSet"'
rangeSampleMeans Average features in ranges per sample
rangeSegMeanLength Get segment widths
rangeSegMeanLength-method Get segment widths
readGenoSet Load a GenoSet from a RData file
rownames-method Get rownames from GRanges, or GenoSet
rownames<--method Get rownames from GRanges, or GenoSet
runCBS Run CBS Segmentation
sampleNames-method Get colnames from a GenoSet
sampleNames<--method Get colnames from a GenoSet
segPairTable Convert Rle objects to tables of segments
segPairTable-method Convert Rle objects to tables of segments
segs2Granges GRanges from segment table
segs2RangedData Make a RangedData from segments
segs2Rle Make Rle from segments for one sample
segs2RleDataFrame CBS segments to probe matrix
segTable Convert Rle objects to tables of segments
segTable-method Convert Rle objects to tables of segments
show-method Print a GenoSet
start-method Get start of location for each feature
subsetAssayData Subset or re-order assayData
toGenomeOrder Set a GRanges or GenoSet to genome order
toGenomeOrder-method Set a GRanges or GenoSet to genome order
universe-method Get universe annotations
universe<--method Get universe annotations
width-method Get width of location for each feature
[-method Subset a GenoSet
[<--method Subset a GenoSet