fx_calcDEvsRest_BP: Internal fx to perform one vs all DE testing using...

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

Internal fx to perform one vs all DE testing using BiocParallel

Description

Internal function. See CalcDEvsRest.

Usage

fx_calcDEvsRest_BP(nge, cl, deTes)

Arguments

nge	The log-normalized gene expression matrix.
cl	The factor with cluster assignments per cell (column of nge).
deTes	The output from fx_calcESvsRest.

Details

Calculates Wilcoxon rank-sum tests for all genes in each one-vs-all comparison of a cluster vs the rest of the data. You probably don't need to use this unless you're trying to customize clusterWiseDEtest.

Value

Differential testing results from Wilcoxon rank sum tests comparing a gene in each cluster to the rest of the cells as a whole in a one vs all comparison. The results are stored as a named list of dataframes. There is a list element for each cluster containing a dataframe of three variables, where each sample is a gene. logGER is the log gene expression ratio calculated by subtracting the mean expression of the gene (see meanLogX for mean calculation) in all other cells from the mean expression of the gene in this cluster. Wstat and pVal are the test statistic and the p-value of the Wilcoxon rank sum test. FDR is the false discovery rate-corrected p-value of the test.

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