gffTrimTranscripts: Trims transcripts in annotation data.frames
In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

gffTrimTranscripts

R Documentation

Trims transcripts in annotation data.frames

Description

Trims transcripts in annotation data.frames of gtf or gff format.

Usage

gffTrimTranscripts(gff, maxLength = 100, start = TRUE)

gffTrimSingleTranscript(gffSingle, maxLength = 100, start = TRUE)

Arguments

`gff`	an annotation data.frame in gtf or gff format.
`maxLength`	an integer specifying the maximum length of transcripts after trimming.
`start`	a logical indicating the start direction of each transcript to be trimmed.
`gffSingle`	the annotation information for a single transcript.

Value

Returns

Functions

gffTrimSingleTranscript: Trims a single transcript according to maxLength and in reversed order depending on the strand (+ / -).

Author(s)

Rehrauer, Hubert

Schmid, Peter

Examples

param = ezParam()
gtf = ezLoadFeatures(param, system.file("extdata/genes.gtf", package="ezRun", mustWork=TRUE))
gtfTrimmed = gffTrimTranscripts(gtf[gtf$type == "exon", ])

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.