cnvMatrix: Retrieve CNV matrix

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

Description

Retrieve CNV matrix from a PatCNVData-class object

Usage

cnvMatrix(obj, sample.name = NULL, gene.name = NULL, 
          chr = NULL, pos.range = NULL, 
          exon.score.vec = NULL, min.exon.score = NULL,
          capture.only = FALSE, 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
exon.ID.format	"gene+pos" or "pos" indicating how to format exon IDs

Value

a data matrix of exon by sample log2-ratio CNV values

Author(s)

Chen Wang

See Also

retrive coverage matrix coverageMatrix

Examples

#=== load simulated data with pre-computed coverage and CNV
data(sim.cnvData)

#=== display CNV log2ratio of exons of gene "SLC25A17" of samples "n2" and "n5"
cnvMatrix(sim.cnvData, c("n2","n5"),"SLC25A17")

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