calc_GICC_gene_sets: calc_GICC_gene_sets

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

Description

Calculates GICC for normalized counts given a list of gene sets.

Usage

calc_GICC_gene_sets(
  counts,
  gene_sets,
  plasmid_sample_id,
  control_sample_id,
  treat_sample_id = NULL
)

Arguments

counts	A data frame of normalized counts for each sample in the study (samples as columns, gRNAs as rows).
gene_sets	A named list of gene sets.
plasmid_sample_id	A character vector naming one or more plasmid samples.
control_sample_id	A character vector naming one or more control samples.
treat_sample_id	A character vector naming one or more treatment samples. If 'NULL' then there are no treatment samples. Defaults to 'NULL'.

Value

A data frame with columns named ‘GICC.<comp>.<gene_set>' where ’<comp>' is one of 'ctrl_plasmid', 'treat_plasmid', or 'treat_ctrl', and '<gene_set>' is the name of each gene set provided in the 'gene_sets' list.

Author(s)

Alex T. Kalinka, [e-mail]

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