goodnessOfFitOnData: Run goodness of fit on a count matrix. It first downsamples...

In chenlab-sj/nbid: Differential expression analysis using negative binomial with independent dispersions (NBID)

Description

Run goodness of fit on a count matrix. It first downsamples all cells to a common total count. Cells with total count less than this threshold will be discarded

Usage

goodnessOfFitOnData(countMatrix, dist = c("nb"),
  downsampleCount = NULL, downsampleQuantile = 0.1, ncore = 1)

Arguments

countMatrix	a gene by cell matrix
dist	a vector of distributions from "poisson", "nb", "zinb"
downsampleCount	the common total count per cell used for downsampling
downsampleQuantile	the quantile of the total count per cell used for downsampling. If downsampleCount is set, this will be ignored. If both are set to NULL, then no downsampling is performed
ncore	the number of cores to use for parallel running

Examples

## Not run: 
load(smallData)
index1 = (smallData$groupLabel == 1)
data1 = smallData$count[, index1]
group1 = smallData$groupLabel[index1]
goodnessResult = goodnessOfFitOnData(data1)
head(goodnessResult)

## End(Not run)

chenlab-sj/nbid documentation built on Nov. 4, 2019, 8:50 a.m.