Construct SCE object from Salmon-Alevin output

Construct SCE object from Salmon-Alevin output

importAlevin(
  alevinDir = NULL,
  sampleName = "sample",
  delayedArray = FALSE,
  class = c("Matrix", "matrix"),
  rowNamesDedup = TRUE
)

Arguments

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 NULL.

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 FALSE.

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".

rowNamesDedup

Boolean. Whether to deduplicate rownames. Default TRUE.

Value

A SingleCellExperiment object containing the count matrix, the feature annotations, and the cell annotation (which includes QC metrics stored in 'featureDump.txt').