Run countsplitting

Fetches specified count matri(ces) from the provided input object, generates countsplit matrices using function countsplit::countsplit() from A. Neufeld, and stores these matrices back in the object with suffixes provided by 'countsplit_suffix'.

Usage

runCountSplit(
  object,
  key = "CHOIR",
  use_assay = NULL,
  use_slot = NULL,
  ArchR_matrix = NULL,
  countsplit_suffix = c("_1", "_2"),
  countsplit_params = list(),
  normalization_method = "log",
  verbose = TRUE
)

Arguments

object

An object of class Seurat, SingleCellExperiment, or ArchRProject. For multi-omic data, we recommend using ArchRProject objects.

key

The name under which CHOIR-related data for this run is stored in the object. Defaults to “CHOIR”.

use_assay

For Seurat or SingleCellExperiment objects, a character string or vector indicating the assay(s) to use in the provided object. The default value, NULL, will choose the current active assay for Seurat objects and the logcounts assay for SingleCellExperiment objects.

use_slot

For Seurat objects, a character string or vector indicating the layers(s) — previously known as slot(s) — to use in the provided object. Default = NULL will use the 'counts' slot.

ArchR_matrix

For ArchR objects, a character string or vector indicating which matrix or matrices to use in the provided object. The default value, NULL, will use the “GeneScoreMatrix” for ATAC-seq data or the “GeneExpressionMatrix” for RNA-seq data. For multi-omic datasets, provide a vector with a value corresponding to each modality.

countsplit_suffix

A character vector indicating the suffixes that distinguish the two count split matrices to be used. Suffixes are appended onto the input string/vector for parameter use_slot for Seurat objects, use_assay for SingleCellExperiment objects, or ArchR_matrix for ArchR objects. Default value NULL uses suffixes "_1" and "_2".

countsplit_params

A list of additional parameters to be passed to countsplit::countsplit().

normalization_method

A character string or vector indicating which normalization method to apply after countsplitting. Permitted values are 'none', 'log', or 'tfidf'. Defaults to 'log'. For multi-omic datasets, provide a vector with a value corresponding to each provided value of use_assay or ArchR_matrix in the same order.

verbose

A Boolean value indicating whether to use verbose output during the execution of CHOIR. Defaults to TRUE, but can be set to FALSE for a cleaner output.

Value

Returns the object including the newly generated countsplit matrices and the following added data stored under the provided key:

parameters

Record of parameter values used