rphast (version 1.6.9)

add.UTRs.feat: Add UTRs to features

Description

Add UTRs to features

Usage

add.UTRs.feat(x)

Arguments

x

An object of type feat. CDS regions must be present with type "CDS", and the transcript_id must be indicated in the attribute field.

Value

An object of type feat, with all the entries of the original object, but also with UTR annotations.

Examples

# NOT RUN {
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
featFile <- "gencode.ENr334.gp"
unzip(exampleArchive, featFile)
f <- read.feat(featFile)
table(f$feature)
coverage.feat(f[f$feature=="CDS",])
coverage.feat(f[f$feature=="exon",])
f <- add.UTRs.feat(f)
table(f$feature)
coverage.feat(f[f$feature=="3'UTR",])
coverage.feat(f[f$feature=="5'UTR",])
unlink(featFile)
# }