Provides classes similar to ExpressionSet for copy number analysis


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Documentation for package ‘genoset’ version 1.20.0

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A B C D E F G I L M N P R S T W misc

genoset-package GenoSet: An eSet for data with genome locations

-- A --

as.matrix-method Class '"RleDataFrame"'

-- B --

baf2mbaf Calculate mBAF from BAF
boundingIndices 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

-- C --

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
coerce-method Class '"RleDataFrame"'
colMeans-method Class '"RleDataFrame"'
colnames-method Get colnames from a GenoSet
colnames<--method Get colnames from a GenoSet
colSums-method Class '"RleDataFrame"'

-- D --

dim-method Dimensions

-- E --

elementLengths-method Get elementLengths from locData slot
end-method Get end of location for each feature

-- F --

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

-- G --

gcCorrect Correct copy number for GC content
genome Get and set the genome universe annotation.
genome-method Genome version
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"'

-- I --

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

-- L --

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

-- M --

modeCenter Center continuous data on mode

-- N --

names-method Get data matrix names
nrow-method Number of rows
numCallable Count Rle positions >= min

-- P --

pos Chromosome position of features
pos-method Chromosome position of features

-- R --

rangeColMeans Calculate summary statistics on views of an RleDataFrame
rangeMaxs Calculate summary statistics on views of an RleDataFrame
rangeMaxs-method Calculate summary statistics on views of an RleDataFrame
rangeMeans Calculate summary statistics on views of an RleDataFrame
rangeMeans-method Calculate summary statistics on views of an RleDataFrame
rangeMins Calculate summary statistics on views of an RleDataFrame
rangeMins-method Calculate summary statistics on views of an RleDataFrame
rangeSampleMeans Average features in ranges per sample
rangeSegMeanLength Get segment widths
rangeSegMeanLength-method Get segment widths
rangeSums Calculate summary statistics on views of an RleDataFrame
rangeSums-method Calculate summary statistics on views of an RleDataFrame
rangeWhichMaxs Calculate summary statistics on views of an RleDataFrame
rangeWhichMaxs-method Calculate summary statistics on views of an RleDataFrame
rangeWhichMins Calculate summary statistics on views of an RleDataFrame
rangeWhichMins-method Calculate summary statistics on views of an RleDataFrame
readGenoSet Load a GenoSet from a RData file
RleDataFrame Class '"RleDataFrame"'
RleDataFrame-class Class '"RleDataFrame"'
RleDataFrame-views Calculate summary statistics on views of an RleDataFrame
rowMeans-method Class '"RleDataFrame"'
rownames-method Get rownames from GRanges, or GenoSet
rownames<--method Get rownames from GRanges, or GenoSet
rowSums-method Class '"RleDataFrame"'
runCBS Run CBS Segmentation

-- S --

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
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 Class '"RleDataFrame"'
show-method Print a GenoSet
start-method Get start of location for each feature
subsetAssayData Subset or re-order assayData

-- T --

toGenomeOrder Set a GRanges or GenoSet to genome order
toGenomeOrder-method Set a GRanges or GenoSet to genome order

-- W --

width-method Get width of location for each feature

-- misc --

[-method Subset a GenoSet
[<--method Subset a GenoSet