addGeneExpressionMatrix.Rd
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, force = TRUE, logFile = createLogFile("addGeneExpressionMatrix") )
input | An |
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seRNA | A a scRNA-seq |
chromSizes | A GRanges object of the chromosome lengths. See |
excludeChr | A character vector containing the |
scaleTo | Each column in the calculated gene score matrix will be normalized to a column sum designated by |
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. |
force | A boolean value indicating whether to force the matrix indicated by |
logFile | The path to a file to be used for logging ArchR output. |