subset_cds: Subset cds by cell group

In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description

subset_cds() subsets a CellDataSet object for a particular cell group and prepares the new CellDataSet subset for the monocle differentialGeneTest() function.

Usage

subset_cds(cell_group, cds, group, min_expr = NULL, read_type = "UMIs")

Arguments

cell_group	string specifying specific cell group e.g. "Rods"
cds	a CellDataSet object used in the monocle package
group	column name in pData(cds) specifying cell group that each cell belong to e.g. "CellType"
min_expr	expression threshold to use for detectGenes() function
read_type	string specifying type of reads in expression matrix; defaults to "UMIs"

Value

CellDataSet object

Examples

subset_cds("Rods", dat, group = "CellType", min_expr = 1)

jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.