anno_import: Import gene annotation

In scPipe: pipeline for single cell RNA-seq data analysis

Description

Because of the variations in data format depending on annotation source, this function has only been tested with human annotation from ENSEMBL, RefSeq and Gencode. If it behaves unexpectedly with any annotation please submit an issue at www.github.com/LuyiTian/scPipe with details.

Usage

anno_import(filename)

Arguments

filename

The name of the annotation gff3 or gtf file. File can be gzipped.

Details

Imports and GFF3 or GTF gene annotation file and transforms it into a SAF formatted data.frame. SAF described at http://bioinf.wehi.edu.au/featureCounts/. SAF contains positions for exons, strand and the GeneID they are associated with.

Value

data.frame containing exon information in SAF format

Examples

ens_chrY <- anno_import(system.file("extdata", "ensembl_hg38_chrY.gtf.gz", package = "scPipe"))

scPipe documentation built on Nov. 8, 2020, 8:28 p.m.