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SoupX (version 1.6.2)

PBMC_sc: 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)

Arguments

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))])