run_mast: Run DGE: 'MAST'

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Run DGE: MAST

Description

Run Differential Gene Expression with MAST.

Usage

run_mast(exp, level2annot, test = "LRT", mtc_method = "BH", no_cores = 1, ...)

Arguments

exp	Expression matrix with gene names as rownames.
level2annot	Array of cell types, with each sequentially corresponding a column in the expression matrix.
mtc_method	Multiple-testing correction method used by DGE step. See p.adjust for more details.
no_cores	Number of cores to parallelise DGE across.
...	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

MAST results

Source

MAST tutorial

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