emptySoup: Estimate expression profile of soup from empty droplets

In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description

emptySoup() is a modified version of the estimateSoup() function in the excellent SoupX package. Instead of using all droplets within the specified soupRange to estimate the expression profile of the soup as per the estimateSoup() function, emptySoup() uses only empty droplets e.g. determined using the testDrops() function to estimate the expression profile of the soup.

Usage

emptySoup(sc, soupRange = c(0, 10), keepDroplets = FALSE)

Arguments

sc	a SoupChannel object created using the createSoupChannel() function implemented in cellwrangler.
soupRange	Droplets with total UMI count in this range (excluding endpoints) are used to estimate soup.
keepDroplets	logical; whether to keep the blankDrops matrix after estimating the soup; defaults to FALSE

Value

a SoupChannel object

Examples

scl <- emptySoup(scl, soupRange = c(0, 10), keepDroplets = FALSE)

jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.