View source: R/MatrixGeneExpression.R
addGeneExpressionMatrix | R Documentation |
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")
)
input |
An |
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. |
strictMatch |
A boolean value indicating whether every cell in |
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. |
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