tidy_annot: Tidy up annotation.

In bartongroup/RATS: Relative Abundance of Transcripts

Tidy up annotation.

Description

With the general english meaning of the word "tidy", not the R Tidyverse meaning.

Usage

tidy_annot(annot, TARGET_COL = "target_id", PARENT_COL = "parent_id")

Arguments

annot	A data.frame matching transcript identifiers to gene identifiers. Any additional columns are allowed but ignored.
TARGET_COL	The name of the column for the transcript identifiers in annot. (Default "target_id")
PARENT_COL	The name of the column for the gene identifiers in annot. (Default "parent_id")

Value

A data.table with genes under parent_id and transcripts under target_id, regardless of what the input annotation named them. Rows ordered first by gene and then by transcript.

Extract the relevant columns as a data.table and order the rows by gene. This creates a fast look-up structure that is consistent throughout RATs.

bartongroup/RATS documentation built on June 8, 2022, 12:40 a.m.