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

Description Usage Arguments Value Note Author(s) Examples

View source: R/feat.R

Description

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

Usage

1

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.

Note

Author(s)

Melissa J. Hubisz and Adam Siepel

Examples

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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)

rphast documentation built on May 30, 2017, 5:13 a.m.

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