Provides classes similar to ExpressionSet for copy number analysis

Documentation for package ‘genoset’ version 1.10.1

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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.to.ExpressionSets	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
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.
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"'
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.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	Functions deprecated in genoset
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
lrr	Get lrr data
lrr-method	Get lrr data
lrr<-	Get lrr data
lrr<--method	Get lrr data

-- M --

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 --

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.