Add Gene Expression Matrix to ArrowFiles or an ArchRProject

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.

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, 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.