add_bagel_ROC_gene_sets: add_bagel_ROC_gene_sets

In alex-kalinka-cruk/fgcQC: QC metric calculations for CRISPR screen data produced at the FGC

Description

Adds True Positive and False Positive columns to Bagel output for a list of gene sets and calculates AUROC for each gene set: all relative to the Hart non-essential genes.

Usage

add_bagel_ROC_gene_sets(bagel_ctrl_pl, bagel_treat_pl, gene_sets)

Arguments

bagel_ctrl_pl	A data frame containing Bagel Bayes Factors results for Control vs Plasmid.
bagel_treat_pl	A data frame containing Bagel Bayes Factors results for Treatment vs Plasmid. Ignored if 'NULL'.
gene_sets	A named list of gene sets.

Value

A list with the following elements: ‘bagel_ctrl_plasmid' - The original data frame with columns 'gene_set', 'True_Positive_Rate.<gene_set>', 'False_Positive_Rate.<gene_set>' where ’<gene_set>' is the name of a gene set. ‘bagel_treat_plasmid' - The original data frame with columns 'gene_set', 'True_Positive_Rate.<gene_set>' and 'False_Positive_Rate.<gene_set>' where ’<gene_set>' is the name of a gene set. 'NULL' if not given. ‘AUROC' - A data frame containing columns 'AUROC.<comp>.<gene_set>' where ’<comp>' is either 'ctrl_plasmid' or 'treat_plasmid' and <gene_set>' is the name of a gene set.

Author(s)

Alex T. Kalinka, [e-mail]

alex-kalinka-cruk/fgcQC documentation built on June 23, 2020, 9:05 p.m.