Provides classes similar to ExpressionSet for copy number analysis

[Up] [Top]

Documentation for package ‘genoset’ version 1.6.0

Help Pages

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

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

-- A --

asFactorMatrix Make factor matrix from character matrix
assayDataElement Get assayDataElement, attaching on-disk resource if necessary
assayDataElement<- Set assayDataElement, attaching on-disk resource if necessary
attachAssayDataElements Attach on-disk matrices into assayData

-- B --

baf Get or Set the baf assayData slot
baf-method BAFSet class
baf.ds Example GenoSet, BAFSet, and CNSet objects and the data to create them.
baf2mbaf Calculate mBAF from BAF
baf<- Get or Set the baf assayData slot
baf<--method BAFSet class
BAFSet Create a BAFSet object
BAFSet-class BAFSet class
bafset-class BAFSet class
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

-- C --

chr Look up chromosome for each feature
chr-method GenoSet class
chrIndices Get a matrix of first and last index of features in each chromosome
chrIndices-method GenoSet class
chrInfo Chromosome Information
chrInfo-method GenoSet class
chrNames Get list of unique chromosome names
chrNames-method GenoSet class
chrOrder Order chromosome names in proper genome order
class:BAFSet BAFSet class
class:CNSet CNSet class
class:GenoSet GenoSet class
cn Get or Set the cn assayData slot
cn-method CNSet class
cn.ds Example GenoSet, BAFSet, and CNSet objects and the data to create them.
cn<- Get or Set the cn assayData slot
cn<--method CNSet class
CNSet Create a CNSet object
CNSet-class CNSet class
cnset-class CNSet class
coerce-method BAFSet class
coerce-method CNSet class
colMeans Means of columns
colMeans-method GenoSet class
convertToBigMatrix Make standard matrices in a GenoSet filebacked bigmatrix objects

-- E --

elementLengths Get space factor for GenoSet
elementLengths-method GenoSet class
end Get space factor for GenoSet
end-method GenoSet class

-- 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<- Set featureNames
featureNames<--method GenoSet class

-- G --

gcCorrect cgCorrect
genomeAxis Label axis with base pair units
genoPlot Plot data along the genome
genoPlot-method Plot data along the genome
genoPos Convert chromosome positions to positions from start of genome
genoPos-method GenoSet class
GenoSet Create a GenoSet object
genoset GenoSet: An eSet for data with genome locations
GenoSet-class GenoSet class
genoset-class GenoSet class
genoset-datasets Example GenoSet, BAFSet, and CNSet objects and the data to create them.
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 --

loadGC Load local GC percentage around features
loadGC-method Load local GC percentage around features
locData Get and set probe set info
locData-method GenoSet class
locData.rd Example GenoSet, BAFSet, and CNSet objects and the data to create them.
locData<- Get and set probe set info
locData<--method GenoSet class
lrr Get or Set the lrr assayData slot
lrr-method BAFSet class
lrr<- Get or Set the lrr assayData slot
lrr<--method BAFSet class

-- M --

modeCenter Center continuous data on mode

-- N --

names Get space factor for GenoSet
names-method GenoSet class

-- O --

orderedChrs-method GenoSet class

-- P --

pos Positions for features
pos-method GenoSet class

-- R --

rangeColMeans Calculate column means for multiple ranges
ranges Get space factor for GenoSet
ranges-method GenoSet class
rangeSampleMeans Average features in ranges per sample
readGenoSet Load a GenoSet from a RData file
relocateAssayData Update "desc" attributes for big.matrix assayDataElement to new location
runCBS Run CBS Segmentation

-- S --

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 GenoSet class
space Get space factor for GenoSet
space-method GenoSet class
start Get space factor for GenoSet
start-method GenoSet class
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 --

uniqueChrs-method GenoSet class
universe Get and set the genome universe annotation.
universe-method GenoSet class
universe<- Get and set the genome universe annotation.
universe<--method GenoSet class

-- W --

width Get space factor for GenoSet

-- misc --

[ Get space factor for GenoSet
[-method GenoSet class
[<- Get space factor for GenoSet
[<--method Get space factor for GenoSet