rphast (version 1.6.9)

add.signals.feat: Add start/stop codon, 3'/5' splice signals to features

Description

Add start/stop codon, 3'/5' splice signals to features

Usage

add.signals.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 stop codons, start, codons, 3' splice, and 5' splice sites annotated.

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$feature=="exon",])
f <- add.signals.feat(f)
table(f$feature)
coverage.feat(f[f$feature=="3'splice",])
coverage.feat(f[f$feature=="5'splice",])
coverage.feat(f[f$feature=="start_codon",])
coverage.feat(f[f$feature=="stop_codon",])
unlink(featFile)
# }