Provides classes similar to ExpressionSet for copy number analysis


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Documentation for package ‘genoset’ version 1.14.0

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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
baf2mbaf Calculate mBAF from BAF
baf<- Get baf data
baf<--method Get baf data
BAFSet Create a BAFSet object
BAFSet-class Class '"BAFSet"'
BAFSet-defunct Create a BAFSet object
BAFSet.to.ExpressionSets Make a pair of ExpressionSets from a BAFSet
BAFSet.to.ExpressionSets-defunct 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 --

calcGC Calculate GC Percentage in windows
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
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-defunct Create a CNSet object
colMeans Means of columns
colMeans-method Means of columns
colnames Get colnames from a GenoSet
colnames-method Get colnames from a GenoSet

-- D --

dim Get start of location for each feature
dim-method Get start of location for each feature

-- E --

elementLengths Get start of location for each feature
elementLengths-method Get start of location for each feature
end Get start of location for each feature
end-method Get start 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 Get rownames from RangedData, GRanges, or GenoSet
featureNames-method Get rownames from RangedData, GRanges, or GenoSet
featureNames<- Get rownames from RangedData, GRanges, or GenoSet
featureNames<--method Get rownames from RangedData, 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 Get and set the genome universe annotation.
genome<--method Get and set the genome universe annotation.
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-defunct Defunct genoset features
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<- 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 start of location for each feature
names-method Get start of location for each feature
nrow Get start of location for each feature
nrow-method Get start of location for each feature

-- P --

pos Positions for features
pos-method Positions for features

-- R --

rangeColMeans Calculate column means for multiple ranges
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 Get rownames from RangedData, GRanges, or GenoSet
rownames-method Get rownames from RangedData, GRanges, or GenoSet
rownames<- Get rownames from RangedData, GRanges, or GenoSet
rownames<--method Get rownames from RangedData, GRanges, or GenoSet
runCBS Run CBS Segmentation

-- S --

sampleNames Get colnames from a GenoSet
sampleNames-method Get colnames from a GenoSet
sampleNames<- 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 Show a GenoSet
show-method Show a GenoSet
start Get start of location for each feature
start-method Get start of location for each feature
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-method Get and set the genome universe annotation.
universe<--method Get and set the genome universe annotation.

-- W --

width Get start of location for each feature

-- misc --

[ Get start of location for each feature
[-method Get start of location for each feature
[<- Get start of location for each feature
[<--method Get start of location for each feature