make_tx_gene_map: I keep messing up the creation of the salmon trancript to...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

I keep messing up the creation of the salmon trancript to gene map.

Description

Maybe this will help. I have a smarter but much slower method in the tmrc3 data which first creates an expressionset without annotations then cross references the rownames against combinations of columns in the annotations to figure out the correct pairing. This helps when I have a combined transcriptome and get confused.

Usage

make_tx_gene_map(
  annotations,
  gene_column = "ensembl_gene_id",
  transcript_column = "ensembl_transcript_id",
  tx_version_column = "transcript_version",
  new_column = "salmon_transcript"
)

Arguments

annotations	Annoation database to merge.
gene_column	Column containing the gene IDs.
transcript_column	Column containing the transcript IDs.
tx_version_column	Salmon uses tx version numbers, find them here.
new_column	Add the new combined IDs here.

Details

This probably doesn't belong in this file.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.