exonInfo: Retrieve exon information

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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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

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#=== 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 16, 2017, 11:26 p.m.