getGeneMatrix: Generate Gene Matrix by directly mapping fragments onto...

In beyondpie/smmtools: Single-cell multi-omics sequenceing data tools

Generate Gene Matrix by directly mapping fragments onto genes.

Description

FIXME: this function should be wrong at somewhere since it's not consistante with SnapATAC

Usage

getGeneMatrix(
  rawH5File,
  outfile,
  barcodes,
  genes = NULL,
  genenms = NULL,
  genome = "mm10",
  sampleName = NULL,
  excludeChr = c("chrM"),
  compressLevel = 9
)

Arguments

rawH5File	string
outfile	string
barcodes	vector of string, neccesary
genes	GenomicRanges, default is NULL, will load automatically using data under the package Otherwise supported by the user.
genenms	vector of string, names of genes, default is NULL If we used the genes by ourselves, and genenms is NULL, we use genes$symbol to get the genenms. This might be error: for example, if we use rtracklayer::import to generate the genes, then they use genes$name to store gene names. So we need to check this mannually.
genome	string, dfeault is "mm10"
sampleName	string, default is NULL
excludeChr	vector of string, default is c("chrM")
compressLevel	integer, used for rhdf5, default is 9.

Value

sparseMatrix, gene by cell

beyondpie/smmtools documentation built on July 1, 2022, 4:33 a.m.