import_quant_data: Import Gene Expression Quantification Data for Single-Cell...

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

Import Gene Expression Quantification Data for Single-Cell RNA-Seq

Description

Imports the gene x cell matrix output from either Alevin, Alevin-fry, Cell Ranger, or Kallisto and returns a SingleCellExperiment.

Usage

import_quant_data(
  quant_dir,
  tool = c("cellranger", "alevin", "alevin-fry", "kallisto"),
  include_unspliced = TRUE,
  usa_mode = FALSE,
  filter = FALSE,
  fdr_cutoff = 0.01,
  tech_version = NULL,
  ...
)

Arguments

quant_dir	Path to directory where output files are located.
tool	Type of tool used to create files (alevin, alevin-fry, cellranger, or kallisto).
include_unspliced	Whether or not to include the unspliced reads in the counts matrix. If TRUE, the main "counts" assay will contain unspliced reads and spliced reads and an additional "spliced" assay will contain spliced reads only. If TRUE, requires that data has been aligned to a reference containing spliced and unspliced reads. Default is TRUE.
usa_mode	Logical indicating if Alevin-fry was used, if the USA mode was invoked. Default is FALSE.
filter	Logical indicating whether or not to filter the counts matrix. Filtering is performed using DropletUtils::emptyDrops and cannot be performed with Cell Ranger.
fdr_cutoff	FDR cutoff to use for DropletUtils::emptyDrops. Default is 0.01.
tech_version	Technology or kit used to process library (i.e. 10Xv3, 10Xv3.1).
...	Any arguments to be passed into DropletUtils::emptyDrops.

Value

SingleCellExperiment of unfiltered gene x cell counts matrix

Examples

## Not run: 
# read in single cell RNA seq data processed using cellranger
import_quant_data(quant_dir,
  tool = "cellranger"
)

# read in single-cell RNA seq data processed using alevin-fry in USA mode
# with alignment to cDNA only and including counts for spliced cDNA only
import_quant_data(quant_dir,
  tool = "alevin-fry",
  include_unspliced = FALSE,
  usa_mode = TRUE
)

# read in single-nuclei RNA-seq data processed using alevin-fry in
# USA mode with alignment to cDNA + introns and including counts for
# unspliced cDNA and perform filtering
import_quant_data(quant_dir,
  tool = "alevin-fry",
  usa_mode = TRUE,
  filter = TRUE
)

# read in single-nuclei RNA-seq data processed using kallisto with
# alignment to cDNA + introns and including counts for unspliced cDNA
# and perform filtering
import_quant_data(quant_dir,
  tool = "kallisto",
  filter = TRUE
)

## End(Not run)

AlexsLemonade/scpcaTools documentation built on July 12, 2024, 8:34 a.m.