createMultiSoupChannel: Create multiple Soup Channels from an cellranger-aggregated...

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

Description

createMultiSoupChannel() is a wrapper function around the createSoupChannel() function that creates a channel for each sample in a matrix aggregated from multiple samples with the cellranger pipeline. The function requires a AllBlankDrops object, which is a matrix consisting of the empty droplets from all samples derived from the original cellranger-aggregated raw matrix using the testDrops() function. Based on the excellent SoupX package.

Usage

createMultiSoupChannel(cds, AllBlankDrops, channelNames = NULL,
  soupRange = c(0, 10))

Arguments

cds	a CellDataSet object (e.g. used in the monocle package)
AllBlankDrops	an expression matrix of empty droplets from all samples in the cellranger aggregate. Matrix must contain barcodes from all the different samples used to form the cellranger aggregate; this can be derived from the original aggregated raw matrix using the testDrops function. Expression values from the AllBlankDrops matrix are used to estimate the soup.
channelNames	vector of strings; channel names to use for all the channels in the sample; number of channel names must equal number of samples used in the cellranger aggregate
soupRange	Droplets with total UMI count in this range (excluding endpoints) are used to estimate soup.

Value

a SoupChannel object with multiple channels (corresponding to number of samples)

Examples

scl <- createMultiSoupChannel(cds=dat, AllBlankDrops=raw_mtx[,all_blank_barcodes], channelNames=NULL
soupRange=c(0,10))

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