fx_calcESvsRest_BP: Internal fx to calculate logGER for DEvsRest calculation...

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

Internal fx to calculate logGER for DEvsRest calculation using BiocParallel

Description

Internal function. See CalcDEvsRest.

Usage

fx_calcESvsRest_BP(nge, cl, CGS, exponent, pseudocount, DRthresh)

Arguments

nge	The log-normalized gene expression matrix.
cl	The factor with cluster assignments per cell (column of nge).
CGS	The output from CalcCGS.
exponent	A length-one numeric vector representing the base of the log-normalized gene expression data to be processed. Generally gene expression data is transformed into log2 space when normalizing (set this to 2), though Seurat uses the natural log (set this to exp(1)). If you are using data that has not been log-transformed (for example, corrected counts from SCTransform), set this to NA.
pseudocount	A length-one numeric vector representing the pseudocount added to all log-normalized values in your input data. Most methods use a pseudocount of 1 to eliminate log(0) errors. If you are using data that has not been log-transformed (for example, corrected counts from SCTransform), set this to NA.
DRthresh	The threshold for minimum detection rate of a gene in the cluster for the gene to be considered in the following Wilcoxon rank-sum test.

Details

Calculates the log-ratios of gene expression for all genes in each one-vs-all comparison of a cluster vs the rest of the data. This is used to determine the genes used in DEvsRest calculations.

Value

The function returns a list where each list element is the log-ratios of gene expression when comparing each gene in a cluster to the rest of the cells as a whole in a one vs all comparison. These logGER tables are filtered to only include those gene that pass logGER threshold, and thus the names for each list entry correspond to the genes to test in fx_calcDEvsRest.

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