exonInfo: Retrieve exon information

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

Description

This function retrieves exon information from an object of PatCNVSession-class or PatCNVData-class

Usage

exonInfo(obj, gene.name = NULL, capture.only = FALSE, attri = NULL)

Arguments

obj	an object of PatCNVData-class
gene.name	a character vector containing gene names. A value of NULL instructs the function to select all the genes
capture.only	a logical value indicating if only captured exons should be outputted
attri	NULL or a character vector containing specified exon attributes

Value

If attri=NULL, a data.frame of exon information is outputted (each row is an exon):

gene.name	gene name or identifier of corresponding exon
chr	exon chromosome
start	exon start position
start	exon end position
is.captured	a binary value, whether this exon is captured

otherwise, a data.frame of specified exon attributes is outputted

Author(s)

Chen Wang

See Also

exonNum, sampleInfo

Examples

#=== load a simulation example
config.filename <- "sim1.ini"
makeSimulation(config.filename)
sim.session <- createSession(config.filename)

#=== print first parts of exon information
head(exonInfo(sim.session))

#=== print first parts of exon information with selected attributes
head(exonInfo(sim.session,attri=c("gene.name","chr","start"))) 

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