createSoupChannel: Create a single Soup Channel

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

Description

createSoupChannel is a modified version of the SoupChannel() function in the excellent SoupX package. Instead of using a table of droplets (tod) that include all droplets to estimate the "soup", createSoupChannel feeds an expression matrix consisting of only empty droplets, determined by the testDrops() function, to estimate the soup in the sample.

Usage

createSoupChannel(blankDrops, cells, channelName, soupRange = c(0, 10),
  keepDroplets = FALSE, ...)

Arguments

blankDrops	an expression matrix of empty droplets derived from the original raw matrix using the testDrops() function. Expression values from the blankDrops matrix are used to estimate the soup using the emptySoup() function.
cells	an expression matrix of cells (e.g. determined by the testDrops() function)
channelName	string; the name of the channel
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 <- createSoupChannel(blankDrops=raw_mtx[,blank_barcodes], cells=raw_mtx[,cell_barcodes], channelNames=NULL
soupRange=c(0,10))

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