PBMC_sc: SoupChannel from PBMC data

In SoupX: Single Cell mRNA Soup eXterminator

SoupChannel from PBMC data

Description

SoupChannel created from 10X demonstration PBMC 4k data. The cells have been sub-sampled by a factor of 2 to reduce file size of package.

Usage

data(PBMC_sc)

Format

PBMC_sc is a SoupChannel object with 33,694 genes and 2,170 cells.

Details

PBMC_sc was created by running the following commands.

• set.seed(1137)

• tmpDir = tempdir(check=TRUE)

• download.file('http://cf.10xgenomics.com/samples/cell-exp/2.1.0/pbmc4k/pbmc4k_raw_gene_bc_matrices.tar.gz',destfile=file.path(tmpDir,'tod.tar.gz'))

• download.file('http://cf.10xgenomics.com/samples/cell-exp/2.1.0/pbmc4k/pbmc4k_filtered_gene_bc_matrices.tar.gz',destfile=file.path(tmpDir,'toc.tar.gz'))

• untar(file.path(tmpDir,'tod.tar.gz'),exdir=tmpDir)

• untar(file.path(tmpDir,'toc.tar.gz'),exdir=tmpDir)

• library(SoupX)

• PBMC_sc = load10X(tmpDir,calcSoupProfile=FALSE)

• PBMC_sc = SoupChannel(PBMC_sc$tod,PBMC_sc$toc[,sample(ncol(PBMC_sc$toc),round(ncol(PBMC_sc$toc)*0.5))])

Source

https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc4k

SoupX documentation built on Nov. 1, 2022, 5:05 p.m.