load10X: Load a collection of 10X data-sets

In constantAmateur/SoupX: Single Cell mRNA Soup eXterminator

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'))

constantAmateur/SoupX documentation built on Nov. 2, 2022, 10:16 a.m.