# Provides classes similar to ExpressionSet for copy number analysis

## Documentation for package ‘genoset’ version 1.16.2

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

## Help Pages

genoset-package | GenoSet: An eSet for data with genome locations
baf2mbaf | Calculate mBAF from BAF
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
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
colMeans | Means of columns
colMeans-method | Means of columns
colnames-method | Get colnames from a GenoSet
colnames<--method | Get colnames from a GenoSet
dim-method | Dimensions
elementLengths-method | Get elementLengths from locData slot
end-method | Get end of location for each feature
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
gcCorrect | Correct copy number for GC content
genome | Get and set the genome universe annotation.
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"'
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
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
modeCenter | Center continuous data on mode
names-method | Get data matrix names
nrow-method | Number of rows
pos | Chromosome position of features
pos-method | Chromosome position of features
rangeColMeans | Calculate column means for multiple ranges
RangedDataOrGenomicRanges-class | Class '"GenoSet"'
RangedDataOrGenoset-class | Class '"GenoSet"'
RangedDataOrGenoSetOrGenomicRanges-class | Class '"GenoSet"'
rangeSampleMeans | Average features in ranges per sample
rangeSegMeanLength | Get segment widths
rangeSegMeanLength-method | Get segment widths
readGenoSet | Load a GenoSet from a RData file
rownames-method | Get rownames from GRanges, or GenoSet
rownames<--method | Get rownames from GRanges, or GenoSet
runCBS | Run CBS Segmentation
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
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 | Print a GenoSet
start-method | Get start of location for each feature
subsetAssayData | Subset or re-order assayData
toGenomeOrder | Set a GRanges or GenoSet to genome order
toGenomeOrder-method | Set a GRanges or GenoSet to genome order
universe-method | Get universe annotations
universe<--method | Get universe annotations
width-method | Get width of location for each feature
[-method | Subset a GenoSet
[<--method | Subset a GenoSet