Provides classes similar to ExpressionSet for copy number analysis


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Documentation for package ‘genoset’ version 1.0.0

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

-- B --

baf Get or Set the baf assayData slot...
baf-method Get or Set the baf assayData slot...
baf-method BAFSet class
baf-methods Get or Set the baf assayData slot...
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 Get or Set the baf assayData slot...
baf<--method BAFSet class
baf<--methods Get or Set the baf assayData slot...
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 chromsome ranges/genes...
boundingIndices2 Find indices of features bounding a set of chromsome ranges/genes...

-- C --

chr Look up chromosome for each feature
chr-method Look up chromosome for each feature
chr-method GenoSet class
chr-methods 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...
chrIndices-method GenoSet class
chrIndices-methods Get a matrix of first and last index of features in each chromosome...
chrInfo Chromosome Information
chrInfo-method Chromosome Information
chrInfo-method GenoSet class
chrInfo-methods Chromosome Information
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 Get or Set the cn assayData slot...
cn-method CNSet class
cn-methods 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...
cn<--method CNSet class
cn<--methods Get or Set the cn assayData slot...
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 Means of columns...
colMeans-method GenoSet class
colMeans-methods Means of columns...

-- E --

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

-- 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<--method GenoSet class

-- G --

gcCorrect cgCorrect
genomeAxis Label axis with base pair units
genomeOrder Get indices to set a RangedData or GenoSet to genome order...
genoPlot genoPlot,-method
genoPlot-method BAFSet class
genoPlot-method CNSet class
genoPlot-method genoPlot,-method
genoPlot-method GenoSet class
genoPlot-methods genoPlot,-method
genoPos Convert chromosome positions to positions from start of genome
genoPos-method Convert chromosome positions to positions from start of genome
genoPos-method GenoSet class
genoPos-methods Convert chromosome positions to positions from start of genome
GenoSet Create a GenoSet object...
genoset Example GenoSet, BAFSet, and CNSet objects and the data to create them.
GenoSet-class GenoSet class
genoset-class GenoSet class
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 RangedData or GenoSet is in genome order...

-- L --

locData Get and set probe set info
locData-method GenoSet class
locData-method Get and set probe set info
locData-methods Get and set probe set info
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
locData<--method Get and set probe set info
lrr Get or Set the lrr assayData slot...
lrr-method BAFSet class
lrr-method Get or Set the lrr assayData slot...
lrr-methods Get or Set the lrr assayData slot...
lrr<- Get or Set the lrr assayData slot...
lrr<--method BAFSet class
lrr<--method Get or Set the lrr assayData slot...
lrr<--methods Get or Set the lrr assayData slot...

-- M --

modeCenter Center continuous data on mode...

-- N --

names Get space factor for GenoSet...
names-method GenoSet class
names-method Get space factor for GenoSet...

-- O --

orderedChrs Get chromosome names in genome order...
orderedChrs-method GenoSet class
orderedChrs-method Get chromosome names in genome order...
orderedChrs-methods Get chromosome names in genome order...

-- P --

pos Positions for features
pos-method GenoSet class
pos-method Positions for features
pos-methods Positions for features

-- R --

ranges Get space factor for GenoSet...
ranges-method GenoSet class
ranges-method Get space factor for GenoSet...
rangeSampleMeans Average features in ranges per sample...
runCBS Run CBS Segmentation

-- S --

segment Run CBS Segmentation
segmentation Run CBS Segmentation
segs2Rle Make Rle from segments for one sample...
segs2RleDataFrame CBS segments to probe matrix
segTable Take a DataFrame of Rle vectors and make a list of data...
show-method GenoSet class
space Get space factor for GenoSet...
space-method GenoSet class
space-method Get space factor for GenoSet...
start Get space factor for GenoSet...
start-method GenoSet class
start-method Get space factor for GenoSet...
subsetAssayData Subset assayData

-- U --

uniqueChrs Get list of unique chromosome names...
uniqueChrs-method GenoSet class
uniqueChrs-method Get list of unique chromosome names...
uniqueChrs-methods Get list of unique chromosome names...
universe Get and set the genome universe annotation.
universe-method GenoSet class
universe-method Get and set the genome universe annotation.
universe<- Get and set the genome universe annotation.
universe<--method GenoSet class
universe<--method Get and set the genome universe annotation.

-- misc --

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