Description Usage Arguments Value Examples
View source: R/createMultiSoupChannel.R
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.
1 2 | createMultiSoupChannel(cds, AllBlankDrops, channelNames = NULL,
soupRange = c(0, 10))
|
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. |
a SoupChannel object with multiple channels (corresponding to number of samples)
1 2 | scl <- createMultiSoupChannel(cds=dat, AllBlankDrops=raw_mtx[,all_blank_barcodes], channelNames=NULL
soupRange=c(0,10))
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.