read_kallisto: Read in counts data processed with Kallisto

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

Read in counts data processed with Kallisto

Description

Read in counts data processed with Kallisto

Usage

read_kallisto(quant_dir, include_unspliced = TRUE, round_counts = TRUE)

Arguments

quant_dir	Path to directory where output files are located.
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.
round_counts	Logical indicating in the count matrix should be rounded to integers on import. Default is TRUE.

Value

SingleCellExperiment of unfiltered gene x cell counts matrix

Examples

## Not run: 

# import output files processed with kallisto with alignment to cDNA + introns,
# including all unspliced cDNA counts in final counts matrix
read_kallisto(quant_dir,
  include_unspliced = TRUE,
  which_counts = "unspliced"
)

## End(Not run)

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