pagoda.effective.cells {scde} | R Documentation

## 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)

[Package scde version 2.8.0 Index]