intronGTFparser: intronGTFparser

In harshsharma-cb/FASE: Analysis of RNA-Sequencing data using FASE (Finding Alternative Splicing Events).

intronGTFparser

Description

Parse intron location given in a gtf file and updated gtf will be written. Intron information can be used then for counting reads with Rsubread package (check wrapper functions: ppAuto and ppSumEIG for read count summarization). However, information associated with these introns (related to transcripts) can not be used as annotation since this transcript information is added in the corresponding field to avoid unnecessary errors.

Usage

intronGTFparser(gtf)

Arguments

gtf	gtf file of the organism.

Value

gtf file with intron information.

References

1. http://Matrix.R-forge.R-project.org/

2. Carey V, Long L, Gentleman R (2019). RBGL: An interface to the BOOST graph library. https://bioconductor.org/packages/RBGL/

3. Gentleman R, Whalen E, Huber W, Falcon S (2019). graph: graph: A package to handle graph data structures. http://www.bioconductor.org/packages/release/bioc/html/graph.html

harshsharma-cb/FASE documentation built on Aug. 6, 2023, 1:37 a.m.