5' splice signals to features
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Note Author(s) Examples

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

1	add.signals.feat(x)

`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.

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.

If x is stored as a pointer to an object stored in C, signals will be added to x.
Does not correctly handle case of splice site in middle of start or stop codon.

Melissa J. Hubisz and Adam Siepel

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)