FindAllIntragroupMarkers: FindAllIntragroupMarkers

In milescsmith/DEGcompareR: Find, plot, and write differentially expressed genes within groups of a Seurat object

Description

Find differentially expressed genes within an identity contrasted by a grouping variable (e.g. comparison between disease status or drug treatment (i.e. compare_by) within each cell type (i.e. ident_use)

Usage

FindAllIntragroupMarkers(object, ident_use, compare_by,
  test_use = "wilcox", min_fold_change = 0, min_pct_express_diff = 0,
  pval_thresh = 0.05, genes_of_interest = NULL,
  cell_number_thresh = 10, pval_use = p_val_adj)

Arguments

object	Processed Seurat scRNAseq object
ident_use	Identity (from the ident slot or a meta.data column) by which to group the cells.
compare_by	Meta.data column by which to group the cells within each identity for comparison.
test_use	Differential expression test to use. Same values as in FindAllMarkers (i.e wilcox, MAST, DESeq2, ...). Default: 'wilcox'
min_fold_change	Minimum log fold change difference between two groups
min_pct_express_diff	Minimum difference in the percentage of each group that expresses the gene in question above a threshold
pval_thresh	Signifigance cutoff for DE testing. Default: 0.05
genes_of_interest	A list of genes to use in DE testing. Default: NULL
cell_number_thresh	Minimum number of cells that must be within an ident.use/group.by grouping before it is discarded. Default: 10
pval_use	p value to use when filtering DE genes by the pval.thresh. Acceptable values are p_val_adj and p_val. Default: p_val_adj

Value

Named list with genes

milescsmith/DEGcompareR documentation built on May 26, 2019, 9:33 a.m.