get_expressed_genes: Find genes expressed in a CellDataSet object

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

Description

get_expressed_genes() finds genes expressed in a CellDataSet object according to defined parameters.

Usage

get_expressed_genes(cds, cell_threshold = 1, min_prop = NULL,
  min_condition = NULL)

Arguments

cds	a CellDataSet object used in the monocle package
cell_threshold	numerical threshold for number of cells that must express a particular gene e.g. 1; if min_prop is specified, this number will be overridden.
min_prop	minimum proportion of cells that must express a particular gene e.g. 0.05 for the gene to be considered expressed
min_condition	a column in pData(cds) that specifies a condition e.g. genotype to which the min_prop argument will be applied; must be specified together with the min_prop argument. Takes the minimum proportion of the condition with fewer cells as the threshold for finding expressed genes.

Value

CellDataSet object

Examples

expressed_genes <- get_expressed_genes(dat, min_prop=0.05, min_condition="genotype")

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