import_gencode_as_txdb: Import gencode GTF file as a TxDb object

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

Description

Import gencode GTF file as a TxDb object

Usage

import_gencode_as_txdb(gtf, filter = NULL)

Arguments

gtf	path of the GTF file
filter	code which filters the GTF records

Details

For example, you can build a TxDb-class object only for protein coding genes by defining

  import_gencode_as_txdb(GTF, gene_type == "protein_coding" & transcript_type == "protein_coding")  

Here gene_type and transcript_type are attributes in the GTF file.

Please note, when building the TxDb-class object, the positions of genes are calculated by the union of all its transcripts, while the positions in the GTF file are not used. This is important when only using a subset of transcripts for a gene (e.g. only use protein coding transcripts) that the position of the gene may change. So, when number of transcripts for genes change, the corresponding TxDb-class object must be re-generated accordingly.

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.