find_sample_dispersed_genes: Find dispersed genes in each sample in CellDataSet

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

Description

find_sample_dispersed_genes() splits an aggregated cds into separate samples based on the suffix at the end of each barcode and estimates SizeFactors and Dispersions for each sample using the package monocle. The function then proceeds to extract genes above pre-specified mean expression and dispersion empirical thresholds

Usage

find_sample_dispersed_genes(cds, mean_exprs = 0, disp_empirical = 1)

Arguments

cds	a monocle CellDataSet object
mean_exprs	mean expression threshold for defining dispersed genes
disp_empirical	dispersion empirical threshold for defining dispersed genes

Value

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

Examples

find_sample_dispersed_genes(dat, mean_exprs=0, disp_empirical=1)

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