Construct SCE object from Salmon-Alevin output
importAlevin(
alevinDir = NULL,
sampleName = "sample",
delayedArray = FALSE,
class = c("Matrix", "matrix"),
rowNamesDedup = TRUE
)
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 NULL
.
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'.
Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default FALSE
.
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".
Boolean. Whether to deduplicate rownames. Default
TRUE
.
A SingleCellExperiment
object containing the count
matrix, the feature annotations, and the cell annotation
(which includes QC metrics stored in 'featureDump.txt').