coverageMatrix: Retrieve coverage matrix

In hshdndx/new-to-CNV: patternCNV: a versatile tool for detecting copy number changes from exome-seq data

Description

Retrieve a raw or normalized coverage data matrix from a PatCNVData-class object

Usage

coverageMatrix(obj, sample.name = NULL, gene.name = NULL,
               chr = NULL, pos.range = NULL, exon.score.vec = NULL,
               min.exon.score = NULL, capture.only = FALSE, 
               type = c("RPKM"), exon.ID.format = "gene+pos")

Arguments

obj	an object of PatCNVData-class
sample.name	a character vector containing sample names. A value of NULL instructs the function to select all the samples
gene.name	a character vector containing gene names. A value of NULL instructs the function to select all the genes
chr	selected chromosome
pos.range	a numeric vector of two values indicating start and end positions of selected chromosome
exon.score.vec	a numeric vector of per-exon confidence score
min.exon.score	minimum exon confidence score
capture.only	a logical value indicating if only captured exons should be used
type	"RPKM" or "raw". default "RPKM" refers to normalized coverage, and "raw" refers to original BP-level coverage
exon.ID.format	"gene+pos" or "pos" indicating how to format exon IDs

Value

a data matrix of exon by sample coverage

Author(s)

Chen Wang

See Also

retrieve CNV data matrix cnvMatrix

Examples

#=== load simulated data with pre-computed coverage information
data(sim.covgData)

#=== list coverage information of a few top exons of sample "n3" and "n5"
head(coverageMatrix(sim.covgData, c("n3","n5")))

hshdndx/new-to-CNV documentation built on May 17, 2019, 5:55 p.m.