calc_log2_fold_change_gRNAs: calc_log2_fold_change_gRNAs

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

Description

Calculates log2 fold changes for sgRNAs from normalized counts. Median counts are taken across replicates.

Usage

calc_log2_fold_change_gRNAs(counts, ref, comp, pseudo_count = 5)

Arguments

counts	A data frame of normalized sgRNA counts for each sample in the study (samples as columns, gRNAs as rows).
ref	A character vector naming the reference sample(s).
comp	A character vector naming the comparison sample(s) to be contrasted against 'ref' samples.
pseudo_count	A small integer specifying a pseudo-count to add to the counts to avoid log2(0) cases. Defaults to 5.

Value

A data frame of log2 fold changes in which the columns are samples and the rows are sgRNAs.

Author(s)

Alex T. Kalinka, [e-mail]

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