NNMD_robust: NNMD_robust

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

Description

Calculates a robust equivalent of the Null-Normalized Mean Difference (NNMD; also known as Glass's delta) for the log fold change distributions of essential and non-essential genes - defined as the median difference divided by the median absolute deviation (MAD) of non-essential genes (the reference set).

Usage

NNMD_robust(data, gene_col, lfc_col, essential_genes, nonessential_genes)

Arguments

data	A data fram containing log fold change data (normalized in terms of library depth and any potential copy-number effects) for a set of genes.
gene_col	A character string indicating which column contains gene names.
lfc_col	A character string indicating which column contains $log_2$ fold change data for each gene.
essential_genes	A vector of essential gene names.
nonessential_genes	A vector of non-essential gene names.

Value

A single numeric value.

Author(s)

Alex T. Kalinka, [e-mail]

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