Provides classes similar to ExpressionSet for copy number analysis

Documentation for package ‘genoset’ version 1.0.0

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-- 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 --

-- 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 --

Center continuous data on mode...

-- N --

-- 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 --

-- 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 --