add_screens_from_table: Adds a list of screens from a sample table file

In HenryWard/orthrus: Scoring Combinatorial CRISPR Screens

Adds a list of screens from a sample table file

Description

For a sample table formatted as a .tsv file with columns for screen, replicates, and the name of a screen to compute log fold-changes against, adds each screen to a list and returns that list. The sample table can be either a path to a .tsv file or a dataframe with the columns mentioned below.

Usage

add_screens_from_table(sample_table)

Arguments

sample_table

Either a dataframe or a path to a .tsv file with three columns: Screen, Replicates, and NormalizeTo. Screen is the name of the screen, replicates are each technical replicate separated by semicolons, and NormalizeTo is either the screen to normalize against or NA if unnecessary (e.g. for T0 screens).

Value

A named list corresponding to provided screen names, where each sub-list contains a list of the replicate columns (in "replicates") and the screen to normalize against (in "normalize_name").

HenryWard/orthrus documentation built on June 2, 2023, 10:28 p.m.