FragInRegions: FragInRegions

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

FragInRegions

Description

Compute total fragment counts in genomic regions for update single cell information table.

Usage

FragInRegions(
  fragment = NULL,
  GR = NULL,
  csvFile = NULL,
  csvOutputFile = NULL,
  name = NULL,
  process_n = 2000
)

Arguments

fragment	A fragment object.
GR	Genomic regions saved in Granges.
csvFile	The csv file used for saving single cell information.
csvOutputFile	The updated csv file.
name	The column name of new data.
process_n	Number of regions to load into memory at a time, per thread. Processing more regions at once can be faster but uses more memory. Default: 5000.

Value

a vector of counts number for every cells.

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.