match_by_gencode: Filter one GTF annotation by another

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Filter one GTF annotation by another

Usage

match_by_gencode(gtf1, gtf2, filter = NULL)

Arguments

gtf1	path for GTF file 1
gtf2	path for GTF file 2
filter	code which additionally filters recodes in gtf1

Details

In some senarios, the analysis was done with an old version of Gencode and it is impossible to redo it with a new version of Gencode (e.g. you dont have access to the original bam files). The only way is to remove those gene/transcript annotations which are not consistent in the two versions. This match_by_gencode function only keeps genes/transcripts that have same gene ids and positions in the two versions.

Similar as import_gencode_as_txdb, filter argument can be used to e.g. only mathch protein coding genes/transcripts.

Value

a TxDb-class object

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
NULL

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.