getGmatFromSnap: Get Gmat from Snap object

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

Get Gmat from Snap object

Description

Get Gmat from Snap object

Usage

getGmatFromSnap(
  snapFile,
  geneBedFile = NULL,
  ibarcode = NULL,
  blacklistBedFile = NULL,
  outfile = NULL,
  compressLevel = 9
)

Arguments

snapFile	string
geneBedFile	string, default is NULL. Only used for mapping with blacklist
ibarcode	vector of string, the barcodes we want to, we assume all of them are in this snapFile. So use this carefully.
blacklistBedFile	string, bed file of the blacklist, smmtools save one under data dir for mm10.
outfile	string, default is NULL, otherwise please end of .h5, and the function will save gmat. if the file already exists, the function will delete it.
compressLevel	integer, default is 9, used for rhdf5.

Value

sparseMatrix, cell by feature, with both row and colname and ordered by ibarcode if provided

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