FindDEgenes: Find markers (differentially expressed genes) among groups.

In YeehanXiao/STREAM: STREAM: Spatial Transcriptomics data Analyses and Modeling

Find markers (differentially expressed genes) among groups.

Description

Find markers (differentially expressed genes) among groups.

Usage

FindDEgenes(counts, annotation, pval = 0.01, logFC = 0.5, minGenes = 10, ...)

Arguments

counts	Either a matrix-like object with un-normalized data with cells as columns and features as rows or an Assay-derived object.
annotation	A data frame of cell types annotation with cell names as rownames and "annot" as the colname. Row-names in the annotation need to match the column names of the counts matrix.
pval	minimal p-value to filter markers
logFC	logFC to filter markers
minGenes	minimum genes to keep in each group per cluster, overrides pval and logFC

YeehanXiao/STREAM documentation built on Aug. 13, 2022, 6:43 p.m.