mcFindAllMarkers: Run FindAllMarkers() on multiple cores

In weshorton/wrh.rUtils: Miscellaneous R Utility Functions

Run FindAllMarkers() on multiple cores

Description

Adapted from https://gist.github.com/diazdc/1735102c243cd16acb1b1f3fd09a26e1 https://github.com/diazdc/seurat-extensions/blob/master/R/cluster_markers.R Instead of running FindAllMarkers, run FindMarkers() in parallel for each cluster.

Usage

mcFindAllMarkers(obj, nCore_v, onlyPos_v = F, test_v = "MAST", latent_v)

Arguments

obj	seurat object. Make sure clusters of interest are set as Idents()
nCore_v	number of cores to split on.
onlyPos_v	logical, passed to only.pos argument in FindMarkers. default F. TRUE - only output positive log2FC markers FALSE - output positive and negative markers
test_v	which test to use. Passed to test.use in FindMarkers
latent_v	vector of latent variables to account for in DE testing.

Value

data.table of markers

weshorton/wrh.rUtils documentation built on Oct. 28, 2024, 7:24 a.m.