read_tx2gene_from_genemap: Read a Salmon "geneMap" file into a data frame

In DarwinAwardWinner/rctutils: Utility functions by Ryan C. Thompson

Read a Salmon "geneMap" file into a data frame

Description

This function reads a file in the Salmon "geneMap" format into a data frame. The format of this file is described in salmon's help text for the "–geneMap" command-line option.

Usage

read_tx2gene_from_genemap(fname)

Arguments

fname

The file to read from. This should generally be a file named "genemap.txt" in a Salmon index directory

Value

A data frame with 2 columns named "TXNAME" and "GENEID".

Since this uses read_table_general() and allows additional columns to be present beyond the first two, it is actually quite lenient about the format of the table.

See Also

The "–geneMap" option to salmon, whose help text describes the format of the file.

DarwinAwardWinner/rctutils documentation built on July 22, 2022, 5:19 a.m.