load10X {SoupX}

Load a collection of 10X data-sets

Description

Loads unfiltered 10X data from each data-set and identifies which droplets are cells using the cellranger defaults.

Usage

load10X(
  dataDir,
  cellIDs = NULL,
  channelName = NULL,
  readArgs = list(),
  includeFeatures = c("Gene Expression"),
  verbose = TRUE,
  ...
)

Arguments

dataDir

Top level cellranger output directory (the directory that contains the raw_gene_bc_matrices folder).

cellIDs

Barcodes of droplets that contain cells. If NULL, use the default cellranger set.

channelName

The name of the channel to store. If NULL set to either names(dataDir) or dataDir is no name is set.

readArgs

A list of extra parameters passed to Seurat::Read10X.

includeFeatures

If multiple feature types are present, keep only the types mentioned here and collapse to a single matrix.

verbose

Be verbose?

...

Extra parameters passed to SoupChannel construction function.

Value

A SoupChannel object containing the count tables for the 10X dataset.

See Also

SoupChannel estimateSoup

Examples

sc = load10X(system.file('extdata','toyData',package='SoupX'))