pagoda.effective.cells: Estimate effective number of cells based on lambda1 of random...

In hms-dbmi/scde: Single Cell Differential Expression

Estimate effective number of cells based on lambda1 of random gene sets

Description

Examines the dependency between the amount of variance explained by the first principal component of a gene set and the number of genes in a gene set to determine the effective number of cells for the Tracy-Widom distribution

Usage

pagoda.effective.cells(pwpca, start = NULL)

Arguments

pwpca	result of the pagoda.pathway.wPCA() call with n.randomizations > 1
start	optional starting value for the optimization (if the NLS breaks, trying high starting values usually fixed the local gradient problem)

Value

effective number of cells

Examples

data(pollen)
cd <- clean.counts(pollen)

knn <- knn.error.models(cd, k=ncol(cd)/4, n.cores=10, min.count.threshold=2, min.nonfailed=5, max.model.plots=10)
varinfo <- pagoda.varnorm(knn, counts = cd, trim = 3/ncol(cd), max.adj.var = 5, n.cores = 1, plot = FALSE)
pwpca <- pagoda.pathway.wPCA(varinfo, go.env, n.components=1, n.cores=10, n.internal.shuffles=50)
pagoda.effective.cells(pwpca)

hms-dbmi/scde documentation built on April 19, 2023, 10:21 p.m.