ensembl_counts_to_rkpm: ensembl_counts_to_rkpm

In Benjamin-Vincent-Lab/PostRNASeqAlign: Functions for writing commands and post processing the Star Salmon pipeline.

ensembl_counts_to_rkpm

Description

Converts an Ensemble ENST counts matrix into RKPM. <rant> RKPM is a terrible way to look at your data. Only do it if you have to. If you choose cDNA length in your calculation then you loose all the non-coding transcripts. If you use the full transcript length then you should account for the number of full and cds sequences which there's no way to know...</rant>

Usage

ensembl_counts_to_rkpm(
  my_dt,
  lengths_table_path = get_human_ensembl_to_hgnc_entrez_path(),
  readme_path = NULL,
  this_script_path = ""
)

Arguments

my_dt	data.table with samples by row, first column should be the sample id with all subsequent columns headers in the Ensembl ENST format (no version).
lengths_table_path	Path to table for with cdna_length and transcript_id columns.
readme_path	Optional path to which the comments will be appended.
this_script_path	Path to script that runs this function for documentation purposes

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ensembl_counts_to_rkpm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Value

A vector of paths to the output file.

Benjamin-Vincent-Lab/PostRNASeqAlign documentation built on Feb. 14, 2024, 8:31 a.m.