Provides classes similar to ExpressionSet for copy number analysis


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Documentation for package ‘genoset’ version 1.12.0

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

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

-- B --

baf Get baf data
baf-method Get baf data
baf.ds Example GenoSet, BAFSet, and CNSet objects and the data to create them.
baf2mbaf Calculate mBAF from BAF
baf<- Get baf data
baf<--method Get baf data
BAFSet Create a BAFSet object
BAFSet-class Class '"BAFSet"'
BAFSet-deprecated Create a BAFSet object
BAFSet.to.ExpressionSets Make a pair of ExpressionSets from a BAFSet
BAFSet.to.ExpressionSets-deprecated Make a pair of ExpressionSets from a BAFSet
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

-- C --

chr Look up chromosome for each feature
chr-method Look up chromosome 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 Chromosome Information
chrInfo-method Chromosome Information
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
cn Get or Set the cn assayData slot
cn-method Get or Set the cn assayData slot
cn.ds Example GenoSet, BAFSet, and CNSet objects and the data to create them.
cn2lr Take vector or matrix of copynumber values, convert to log2ratios Utility function for converting copynumber units (2 is normal) to log2ratio units (two is normal)
cn<- Get or Set the cn assayData slot
cn<--method Get or Set the cn assayData slot
CNSet Create a CNSet object
CNSet-class Class '"CNSet"'
CNSet-deprecated Create a CNSet object
colMeans Means of columns
colMeans-method Means of columns

-- D --

dim Get and set the genome universe annotation.
dim-method Get and set the genome universe annotation.

-- E --

elementLengths Get and set the genome universe annotation.
elementLengths-method Get and set the genome universe annotation.
end Get and set the genome universe annotation.
end-method Get and set the genome universe annotation.

-- 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 Get rownames from RangedData, GRanges, or GenoSet
featureNames-method Get rownames from RangedData, GRanges, or GenoSet
featureNames<- Set featureNames
featureNames<--method Set featureNames
fixSegNAs Fix NA runs in a Rle

-- G --

gcCorrect Correct copy number for GC content
genomeAxis Label axis with base pair units
genoPlot Plot data along the genome
genoPlot-method Plot data along the genome
genoPlot-methods Plot data along the genome
genoPos Convert chromosome positions to positions from start of genome
genoPos-method Convert chromosome positions to positions from start of genome
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-deprecated Deprecated genoset features
genoset.ds Example GenoSet, BAFSet, and CNSet objects and the data to create them.

-- I --

initGenoSet Create a GenoSet or derivative object
isGenomeOrder Check if a GRanges, GenoSet or RangedData is in genome order
isGenomeOrder-method Check if a GRanges, GenoSet or RangedData is in genome order

-- L --

locData Access the feature genome position info
locData-method Access the feature genome position info
locData-methods Access the feature genome position info
locData.gr Example GenoSet, BAFSet, and CNSet objects and the data to create them.
locData.rd 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
locData<--methods Access the feature genome position info
lr2cn Take vector or matrix of log2 ratios, convert to copynumber Utility function for converting log2ratio units (zero is normal) to copynumber units (two is normal)
lrr Get lrr data
lrr-method Get lrr data
lrr<- Get lrr data
lrr<--method Get lrr data

-- M --

modeCenter Center continuous data on mode

-- N --

names Get and set the genome universe annotation.
names-method Get and set the genome universe annotation.
nrow Get and set the genome universe annotation.
nrow-method Get and set the genome universe annotation.

-- P --

pos Positions for features
pos-method Positions for features

-- R --

rangeColMeans Calculate column means for multiple ranges
ranges Get and set the genome universe annotation.
ranges-method Get and set the genome universe annotation.
rangeSampleMeans Average features in ranges per sample
readGenoSet Load a GenoSet from a RData file
runCBS Run CBS Segmentation

-- S --

sampleNames Get sampleNames from a GenoSet
sampleNames-method Get sampleNames from a GenoSet
segPairTable Convert Rle objects to tables of segments
segPairTable-method Convert Rle objects to tables of segments
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 Get and set the genome universe annotation.
show-method Get and set the genome universe annotation.
space Get and set the genome universe annotation.
space-method Get and set the genome universe annotation.
start Get and set the genome universe annotation.
start-method Get and set the genome universe annotation.
subsetAssayData Subset assayData

-- T --

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

-- U --

universe Get and set the genome universe annotation.
universe-method Get and set the genome universe annotation.
universe<- Get and set the genome universe annotation.
universe<--method Get and set the genome universe annotation.

-- W --

width Get and set the genome universe annotation.

-- misc --

[ Get and set the genome universe annotation.
[-method Get and set the genome universe annotation.
[<- Get and set the genome universe annotation.
[<--method Get and set the genome universe annotation.