fx_calcEScombn: Internal fx to calculate genes used for deVS calculation

In BaderLab/scClustViz: Differential Expression-based scRNAseq Cluster Assessment and Viewing

Internal fx to calculate genes used for deVS calculation

Description

Internal function. See CalcDEcombn.

Usage

fx_calcEScombn(cl, CGS, DRthresh)

Arguments

cl	The factor with cluster assignments per cell (column of nge).
CGS	The output from fx_calcCGS.
DRthresh	The threshold for minimum detection rate of a gene to be considered in the following Wilcoxon rank-sum test. Gene must pass threshold in at least one of the pair of clusters.

Details

Calculates the log-ratios of gene expression and difference in detection rate for all genes in each of the potential combinations of clusters to compare. This is used to determine the genes used in deVS calculations.

Value

The function returns a list where each list element is a dataframe with effect size statistics (log-ratios of gene expression and difference in detection rate) when comparing each gene in a cluster to the rest of the cells as a whole in a one vs all comparison. These dataframes are filtered to only include those gene that pass the relevant threshold, and thus the rownames for each list entry correspond to the genes to test in fx_calcDEcombn.

BaderLab/scClustViz documentation built on Sept. 10, 2023, 11:51 p.m.