run_deseq2: Run DGE: 'DESeq2'

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Run DGE: DESeq2

Description

Run Differential Gene Expression with DESeq2.

Usage

run_deseq2(exp, level2annot, test = "LRT", no_cores = 1, verbose = TRUE, ...)

Arguments

exp	Expression matrix with gene names as rownames.
level2annot	Array of cell types, with each sequentially corresponding a column in the expression matrix.
test	either "Wald" or "LRT", which will then use either Wald significance tests (defined by nbinomWaldTest), or the likelihood ratio test on the difference in deviance between a full and reduced model formula (defined by nbinomLRT)
no_cores	Number of cores to parallelise across. Set to NULL to automatically optimise.
verbose	Print messages. #' @inheritParams orthogene::convert_orthologs
...	Additional arguments to be passed to gorth or homologene. NOTE: To return only the most "popular" interspecies ortholog mappings, supply mthreshold=1 here AND set method="gprofiler" above. This procedure tends to yield a greater number of returned genes but at the cost of many of them not being true biological 1:1 orthologs. For more details, please see here.

Value

DESeq results

NathanSkene/EWCE documentation built on Nov. 3, 2024, 8:16 a.m.