groupGff: Groups annotation

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Groups annotation

Description

Groups annotation according to the grouping factor. Duplicated values are dropped and the function checks for transspliced elements.

Usage

groupGff(
  gtf,
  grouping = gtf$Parent,
  type = "transcript",
  skipTransSpliced = FALSE
)

gffGroupToRanges(gtf, grouping, skipTransSpliced = FALSE)

Arguments

gtf	the annotation data.frame to group.
grouping	a vector of the annotation data.frame to group it by.
type	a character representing the new type name.
skipTransSpliced	a logical indicating whether to skip transspliced elements if they exist.

Value

Returns a grouped annotation data.frame.

Functions

• gffGroupToRanges(): Groups annotation and returns a GRanges object from the grouped annotation.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

GRanges

Examples

param = ezParam()
gtf = ezLoadFeatures(param, system.file("extdata/genes.gtf", package="ezRun", mustWork=TRUE))
groupedGtf = groupGff(gtf)
gffGroupToRanges(gtf, grouping = gtf$Parent)

uzh/ezRun documentation built on March 5, 2025, 3:41 p.m.