Description Usage Arguments Details Author(s) Examples
View source: R/transcript_to_gene_fix.R
Given a GTF file with transcript ids in the "gene_id" field and a file mapping these to gene ids, write a new GTF with gene ids in that field.
1 | transcript_to_gene_fix(gtf, mapFile, outSuffix = "_geneids")
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gtf |
String - Name of GTF with transcript ids in gene_id field |
mapFile |
String - Name of csv with gene ids in the first column and transcript ids in the second |
Use the transcript_to_gene_map function to create the mapFile input. TIME: Most of it's the "Replacing transcript ids with gene ids in key-value field" part, which is anywhere from 15-30m.
Emma Myers
1 | transcript_to_gene_fix("/Volumes/CodingClub1/RNAseq/Metadata/mm10_refSeq_introns.gtf", "/Volumes/CodingClub1/RNAseq/Metadata/RefSeq_id_map.csv")
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