sumFragmentSingleThread: Transform original tabix File to H5File, then get...

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

Transform original tabix File to H5File, then get barcodes-related fragments stats.

Description

• Ref: ArchR

• Method is run on single core, but the speed should be OK.

• No filtering barcodes here unless we provide barcode array ourselves.

• Side Effect:

  • output rawH5File

  • output sumFragment File (descreasingly ordered by nUniqFrag)

Usage

sumFragmentSingleThread(
  rawH5File,
  sumFragFile,
  genome,
  sampleName = NULL,
  barcodes = NULL,
  nChunk = 3,
  tsseWindow = 101,
  tsseNorm = 100,
  tsseFlank = 2000,
  tsseMinNorm = 0.2,
  tsseMaxFragSize = NULL
)

Arguments

genome	string, namely mm9, mm10, hg19 or hg38
sampleName	string, name for the tabix file
barcodes	vector of string, limite fragment on specific barcodes
nChunk	integer, partition each chrom into nChunk pieces
tsseWindow	integer
tsseNorm	interger
tsseFlank	integer
tsseMinNorm	float
tsseMaxFragSize	integer
tabixFile	string, 10x cell ranger result tab/tab.gz file name
outfilenm	string, output file name, if NULL, a default one will be genereated.
coverH5File	bool, whether to cover the rawH5File if exists

Value

data.frame with cols: barcode, nUniqFrag, TSSE, TSSReads

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