Learn R Programming
⚠️There's a newer version (1.28.2) of this package.Take me there.

genoset (version 1.24.0)

Provides classes similar to ExpressionSet for copy number analysis

Description

Load, manipulate, and plot copynumber and BAF data. GenoSet class extends eSet by adding a "locData" slot for a GRanges object. This object contains feature genome location data and provides for efficient subsetting on genome location. Provides convenience functions for processing of copy number and B-Allele Frequency data. Provides the class RleDataFrame to store runs of data along the genome for multiple samples.

Copy Link

Version

Version

1.24.0

License

Artistic-2.0

Issues

1

Pull Requests

0

Stars

0

Forks

0

Maintainer

Peter M Haverty

Last Published

February 15th, 2017

Functions in genoset (1.24.0)

chr

Chromosome name for each feature
calcGC2

Calculate GC Percentage in sliding window
genoset-deprecated

Deprecated genoset features
chrNames

Get list of unique chromosome names
chrOrder

Order chromosome names in proper genome order
genoset-defunct

Defunct genoset features
isGenomeOrder

Check if a GRanges orGenoSet is in genome order
locData

Access the feature genome position info
rownames,GenomicRanges-method

Get rownames from GRanges, or GenoSet
runCBS

Run CBS Segmentation
width,GenoSet-method

Get width of location for each feature
toGenomeOrder

Set a GRanges or GenoSet to genome order
bounds2Rle

Convert bounding indices into a Rle
calcGC

Calculate GC Percentage in windows
genoPlot

Plot data along the genome
boundingIndicesByChr

Find indices of features bounding a set of chromosome ranges/genes, across chromosomes
boundingIndices

Find indices of features bounding a set of chromosome ranges/genes
cn2lr

Take vector or matrix of copynumber values, convert to log2ratios
colnames,GenoSet-method

Get colnames from a GenoSet
gcCorrect

Correct copy number for GC content
GenoSet

Create a GenoSet object
initGenoSet

Create a GenoSet or derivative object
genoPos

Get base positions of features in genome-scale units
pos

Chromosome position of features
rangeSampleMeans

Average features in ranges per sample
chrIndices

Get a matrix of first and last index of features in each chromosome
chrInfo

Get chromosome start and stop positions
modeCenter

Center continuous data on mode
genome,GenoSet-method

Genome version
nrow,GRanges-method

Number of rows
numCallable

Count Rle positions >= min
segPairTable

Convert Rle objects to tables of segments
segs2Granges

GRanges from segment table
lr2cn

Take vector or matrix of log2 ratios, convert to copynumber
elementLengths,GenoSet-method

Get elementLengths from locData slot
.do_rledf_views

Calculate min/max/sum/mean/whichmin/whichmax over each view on each column of an RleDataFrame.
genoset-package

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

Example GenoSet, BAFSet, and CNSet objects and the data to create them.
GenoSet-class

Class "GenoSet"
[,GenoSet,ANY-method

Subset a GenoSet
RleDataFrame-views

Calculate summary statistics on views of an RleDataFrame
RleDataFrame-class

Class "RleDataFrame"
start,GenoSet-method

Get start of location for each feature
subsetAssayData

Subset or re-order assayData
end,GenoSet-method

Get end of location for each feature
names,GenoSet-method

Get data matrix names
fixSegNAs

Fix NA runs in a Rle
nrow,GenomicRanges-method

Number of rows
segs2Rle

Make Rle from segments for one sample
segs2RleDataFrame

CBS segments to probe matrix
API

Converting eSet API to RangedSummarizedExperiment
baf2mbaf

Calculate mBAF from BAF
dim,GenoSet-method

Dimensions
.do_rledf_range_summary

Calculate min/max/sum/mean/whichmin/whichmax over ranges on each column of an RleDataFrame.
genome

Get and set the genome universe annotation.
rangeSegMeanLength

Get segment widths
genomeAxis

Label axis with base pair units
readGenoSet

Load a GenoSet from a RData file
segTable

Convert Rle objects to tables of segments
show,GenoSet-method

Print a GenoSet