loadSoupX: Load Data for SoupX

In scfurl/m3addon: This package adds to the popular "monocle3"

Description

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

Usage

loadSoupX(
  dataDir,
  cellIDs = NULL,
  channelName = NULL,
  readArgs = list(),
  includeFeatures = c("Gene Expression"),
  verbose = TRUE,
  method = c("SoupX_10X", "10X_H5", "STARsolo"),
  ...
)

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?
method	type of input data; Use "SoupX_10X" for processing cellranger output, "10X_H5" for processing a folder of H5 cellranger output files, and "STARsolo" for processing STARsolo output.
...	Extra parameters passed to SoupChannel construction function.

Value

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

scfurl/m3addon documentation built on Aug. 9, 2021, 5:30 p.m.