read_alevin: Read in counts data processed with Alevin or Alevin-fry

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

Read in counts data processed with Alevin or Alevin-fry

Description

Read in counts data processed with Alevin or Alevin-fry

Usage

read_alevin(
  quant_dir,
  fry_mode = FALSE,
  include_unspliced = TRUE,
  feature_data = FALSE,
  round_counts = TRUE,
  library_id = NULL,
  sample_id = NULL,
  project_id = NULL,
  tech_version = NULL,
  assay_ontology_term_id = NULL,
  seq_unit = NULL
)

Arguments

quant_dir	Path to directory where output files are located.
fry_mode	Logical indicating if Alevin-fry was used for quantification. Implies the input data is in matrix market format. Default is FALSE.
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.
feature_data	Logical indicating if the data being read in contains feature data. Default is FALSE. If feature data is being read in there are no spliced or unspliced reads. All reads will be counted and stored in the 'counts' assay.
round_counts	Logical indicating in the count matrix should be rounded to integers on import. Only used if 'fry_mode' is FALSE. Default is TRUE.
library_id	Optional library identifier
sample_id	Optional sample identifier. If multiplexed samples are included in a library, this may be a vector.
project_id	Optional project identifier.
tech_version	Technology or kit used to process library (i.e. 10Xv3, 10Xv3.1).
assay_ontology_term_id	Optional Experimental Factor Ontology term associated with the provided 'tech_version'
seq_unit	Optional sequencing unit associated with the library (i.e. cell, nucleus)

Value

SingleCellExperiment of unfiltered gene x cell counts matrix.

Examples

## Not run: 

# Import output files processed with either Alevin or Alevin-fry with alignment to
# cDNA only, including only spliced cDNA in final counts matrix
read_alevin(quant_dir)

# Import output files processed with either Alevin or Alevin-fry with alignment to
# cDNA + introns and including all unspliced cDNA in final counts matrix
read_alevin(quant_dir,
  include_unspliced = TRUE
)

# Import output files processed with alevin-fry USA mode
# including all unspliced cDNA in final counts matrix
read_alevin(quant_dir,
  fry_mode = TRUE,
  include_unspliced = TRUE
)

## End(Not run)

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