coverageMatrix: Retrieve coverage matrix

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

1
2
3
4
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

1
2
3
4
5
#=== 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 16, 2017, 11:26 p.m.