findCells: Estimates which droplets contain a cell

Description Usage Arguments Value

View source: R/findCells.R

Description

This function attempts to identify which droplets contain cells based on the level of contamination in each cell. For this to work well, there must be sufficient power to estimate the contamination fraction in each droplet, which is usually not the case unless spike-ins have been used. To determine which droplets contain cells, a binomial test (with FDR correction) is performed against the NULL hypothesis that the contamination rate is equal to or greater than contCut.

Usage

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findCells(sc, nonExpressedGeneList, useToEst = NULL, minUMIs = 100,
  minGenes = 50, contCut = 0.3)

Arguments

sc

A SoupChannel object for which the table of droplets has been retained. That is, estimateSoup was run with keepDroplets=TRUE.

nonExpressedGeneList

Genes to use for estimating contamination fraction (see calculateContaminationFraction)

useToEst

Which cells to use which sets of genes to estimate contamination (see calculateContaminationFraction)

minUMIs

Don't test any droplet with fewer than this many UMIs.

minGenes

Don't test any droplet with fewer than this many detected genes.

contCut

The maximum allowable contamination fraction for a droplet containing a cell.

Value

A data.frame with contamination fraction estimates for each droplet and a p-value and FDR for rejecting the NULL hypothesis and accepting this droplet as a cell.


constantAmateur/SoupX documentation built on July 23, 2018, 9:20 a.m.