addGeneExpressionMatrix: Add Gene Expression Matrix to ArrowFiles or an ArchRProject

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

Add Gene Expression Matrix to ArrowFiles or an ArchRProject

Description

This function, for each sample, will add gene expression values from a paired scATAC-seq + scRNA-seq multi modal assay to the ArrowFiles or ArchRProject.

Usage

addGeneExpressionMatrix(
  input = NULL,
  seRNA = NULL,
  chromSizes = getChromSizes(input),
  excludeChr = c("chrM", "chrY"),
  scaleTo = 10000,
  verbose = TRUE,
  threads = getArchRThreads(),
  parallelParam = NULL,
  strictMatch = FALSE,
  force = TRUE,
  logFile = createLogFile("addGeneExpressionMatrix")
)

Arguments

input	An ArchRProject object or character vector of ArrowFiles.
seRNA	A a scRNA-seq SummarizedExperiment (cell x gene) to be integrated with the scATAC-seq data. Cell names from this object much match those of the cell names in the ArrowFiles/ArchRProject. We will add support shortly for Seurat Objects (see Seurat::as.SingleCellExperiment). The provided values MUST be in counts (integer), not log transformed.
chromSizes	A GRanges object of the chromosome lengths. See getChromSizes for more info.
excludeChr	A character vector containing the seqnames of the chromosomes that should be excluded from this analysis.
scaleTo	Each column in the calculated gene score matrix will be normalized to a column sum designated by scaleTo.
verbose	A boolean describing whether to print to console messages of progress.
threads	The number of threads to be used for parallel computing.
parallelParam	A list of parameters to be passed for biocparallel/batchtools parallel computing.
strictMatch	A boolean value indicating whether every cell in input must be represented in seRNA. If set to FALSE, this and this GeneExpressionMatrix is used for certain downstream analyses such as addIterativeLSI(), then errors may occur because not all cells will have relevant information.
force	A boolean value indicating whether to force the matrix indicated by matrixName to be overwritten if it already exist in the given input.
logFile	The path to a file to be used for logging ArchR output.

GreenleafLab/ArchR documentation built on Feb. 28, 2024, 4:17 p.m.