# Provides classes similar to ExpressionSet for copy number analysis

## Documentation for package ‘genoset’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

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

## -- A --

as.matrix-method | Class '"RleDataFrame"'

## -- B --

baf2mbaf | Calculate mBAF from BAF
boundingIndices | 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 | Chromosome name for each feature
chr-method | Chromosome name 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 | Get chromosome start and stop positions
chrInfo-method | Get chromosome start and stop positions
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
cn2lr | Take vector or matrix of copynumber values, convert to log2ratios
cn2lr-method | Take vector or matrix of copynumber values, convert to log2ratios
coerce-method | Class '"RleDataFrame"'
colMeans-method | Class '"RleDataFrame"'
colnames-method | Get colnames from a GenoSet
colnames<--method | Get colnames from a GenoSet
colSums-method | Class '"RleDataFrame"'

## -- D --

dim-method | Dimensions

## -- E --

elementLengths-method | Get elementLengths from locData slot
end-method | Get end 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-method | Get rownames from GRanges, or GenoSet
featureNames<--method | Get rownames from 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 | Genome version
genome<--method | Genome version
genomeAxis | Label axis with base pair units
genoPlot | Plot data along the genome
genoPlot-method | Plot data along the genome
genoPos | Get base positions of features in genome-scale units
genoPos-method | Get base positions of features in genome-scale units
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.
GenoSetOrGenomicRanges-class | Class '"GenoSet"'

## -- I --

initGenoSet | Create a GenoSet or derivative object
isGenomeOrder | Check if a GRanges orGenoSet is in genome order
isGenomeOrder-method | Check if a GRanges orGenoSet is in genome order

## -- L --

locData | Access the feature genome position info
locData-method | 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
lr2cn | Take vector or matrix of log2 ratios, convert to copynumber

## -- M --

modeCenter | Center continuous data on mode

## -- N --

names-method | Get data matrix names
nrow-method | Number of rows
nrow-method | Number of rows
numCallable | Count Rle positions >= min

## -- P --

pos | Chromosome position of features
pos-method | Chromosome position of features

## -- R --

rangeColMeans | Calculate summary statistics on views of an RleDataFrame
rangeMaxs | Calculate summary statistics on views of an RleDataFrame
rangeMaxs-method | Calculate summary statistics on views of an RleDataFrame
rangeMeans | Calculate summary statistics on views of an RleDataFrame
rangeMeans-method | Calculate summary statistics on views of an RleDataFrame
rangeMins | Calculate summary statistics on views of an RleDataFrame
rangeMins-method | Calculate summary statistics on views of an RleDataFrame
rangeSampleMeans | Average features in ranges per sample
rangeSegMeanLength | Get segment widths
rangeSegMeanLength-method | Get segment widths
rangeSums | Calculate summary statistics on views of an RleDataFrame
rangeSums-method | Calculate summary statistics on views of an RleDataFrame
rangeWhichMaxs | Calculate summary statistics on views of an RleDataFrame
rangeWhichMaxs-method | Calculate summary statistics on views of an RleDataFrame
rangeWhichMins | Calculate summary statistics on views of an RleDataFrame
rangeWhichMins-method | Calculate summary statistics on views of an RleDataFrame
readGenoSet | Load a GenoSet from a RData file
RleDataFrame | Class '"RleDataFrame"'
RleDataFrame-class | Class '"RleDataFrame"'
RleDataFrame-views | Calculate summary statistics on views of an RleDataFrame
rowMeans-method | Class '"RleDataFrame"'
rownames-method | Get rownames from GRanges, or GenoSet
rownames<--method | Get rownames from GRanges, or GenoSet
rowSums-method | Class '"RleDataFrame"'
runCBS | Run CBS Segmentation

## -- S --

sampleNames-method | Get colnames from a GenoSet
sampleNames<--method | 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
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 | Class '"RleDataFrame"'
show-method | Print a GenoSet
start-method | Get start of location for each feature
subsetAssayData | Subset or re-order assayData

## -- T --

toGenomeOrder | Set a GRanges or GenoSet to genome order
toGenomeOrder-method | Set a GRanges or GenoSet to genome order

## -- W --

width-method | Get width of location for each feature

## -- misc --

[-method | Subset a GenoSet
[<--method | Subset a GenoSet