Construct SCE object from Salmon-Alevin output
importAlevin( alevinDir = NULL, sampleName = "sample", delayedArray = FALSE, class = c("Matrix", "matrix") )
alevinDir | Character. The output directory of salmon-Alevin pipeline.
It should contain subfolder named 'alevin', which contains the count data
which is stored
in 'quants_mat.gz'. Default |
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sampleName | Character. A user-defined sample name for the sample to be imported. The 'sampleName' will be appended to the begining of cell barcodes. Default is 'sample'. |
delayedArray | Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default |
class | Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix". |
A SingleCellExperiment
object containing the count
matrix, the feature annotations, and the cell annotation
(which includes QC metrics stored in 'featureDump.txt').