find_sample_expressed_genes: Find expressed genes in each sample in CellDataSet

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

Description

find_sample_expressed_genes() splits an aggregated cds into separate samples based on the suffix at the end of each barcode. The function then proceeds to extract genes above the pre-specified UMI and cell expression threshold(s)

Usage

find_sample_expressed_genes(cds, UMI_threshold = 1, cell_threshold = 1)

Arguments

cds	a monocle CellDataSet object
UMI_threshold	UMI threshold for defining expressed genes. Genes with total UMIs equal to or above this threshold will be selected.
cell_threshold	cell threshold for defining expressed genes. Genes expressed in a total number of cells at or above this threshold will be selected.

Value

A list of vectors with each vector containing dispersed genes for each sample

Examples

find_sample_expressed_genes(dat,UMI_threshold = 1, cell_threshold = 10)

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