MakeMatrices: Generate matrices for clustering analysis
In noush-joglekar/scisorseqr: Processes long reads for differential isoform analysis

MakeMatrices

R Documentation

Generate matrices for clustering analysis

Converts the counts for isoforms into matrices clustered either by cell-type or by barcode.

MakeMatrices(
  isoQuantOutDir = "IsoQuantOutput/",
  groupBy = "Cell",
  ensemblToClear = NULL,
  convertTo10XoutputFormat = TRUE
)

`isoQuantOutDir`	output directory of IsoQuant function. Defaults to IsoQuantOutput
`groupBy`	String indicating group for matrix output. Current options involve "Cell" or "Celltype", and defaults to "Cell"
`ensemblToClear`	A mapping of gene-names from ENSEMBL ids to human readable gene names for downstream analysis. Defaults to mm10 gencode v21 annotation.
`convertTo10XoutputFormat`	OPTIONAL If grouped by cell, logical inputt indicating whether or not matrix should be converted into a format similar to 10X cellranger output for downstream analysis. Defaults to TRUE