getdge: Obtain EdgeR DGE object from count matrix

In rosedu1/deconvSeq: Cell Type Deconvolution for RNA Sequencing and Bisulfite Sequencing

Description

Obtain EdgeR DGE object from count matrix

Usage

getdge(countmat, design, ncpm.min = 1, nsamp.min = 4, method = "auto")

Arguments

countmat	a matrix of counts with rows corresponding to genes and columns to samples
design	output of model.matrix
ncpm.min	filtering threshold for cpm
nsamp.min	minimum number of samples that must have cpm
method	method used to esimate trended dispersion in EdgeR: "auto" (default), "bin.spline", "bin.loess", "power", "spline" exceeding ncpm.min for a gene to be retained

Value

dge DGE object

Examples

data("data_celltypes_rnaseq") 
dge.celltypes = getdge(cnts.celltypes, design.rnaseq, ncpm.min=1, nsamp.min=4)

rosedu1/deconvSeq documentation built on Aug. 19, 2020, 7:10 p.m.