anno_to_saf: Convert annotation from GenomicRanges to Simple Annotation...

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

Convert annotation from GenomicRanges to Simple Annotation Format (SAF)

Description

This function converts a GRanges object into a data.frame of the SAF format for scPipe's consumption. The GRanges object should contain a "type" column where at least some features are annotated as "exon", in addition there should be a gene_id column specifying the gene to which the exon belongs. In the SAF only the gene ID, chromosome, start, end and strand are recorded, this is a gene-exon centric format, with all entries containing the same gene ID treated as exons of that gene. It is possible to count alternative features by setting the gene_id column to an arbitrary feature name and having alternative features in the SAF table, the main caveat is that the features are still treated as exons, and the mapping statistics for exon and intron will not reflect biological exons and introns but rather the annotation features.

Usage

anno_to_saf(anno)

Arguments

anno	The GRanges object containing exon information

Details

Convert a GRanges object containing type and gene_id information into a SAF format 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

 ## Not run: 
     anno <- system.file("extdata", "ensembl_hg38_chrY.gtf.gz", package = "scPipe")
     saf_chrY <- anno_to_saf(rtracklayer::import(anno))
 
## End(Not run)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.