GetReadsInRegion: Extract reads for each cell within a given genomic region or...

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

Extract reads for each cell within a given genomic region or set of regions

Description

Extract reads for each cell within a given genomic region or set of regions

Usage

GetReadsInRegion(
  cellmap,
  region,
  tabix.file,
  cells = NULL,
  verbose = TRUE,
  ...
)

Arguments

cellmap	A mapping of cell names in the fragment file to cell names in the Seurat object. Should be a named vector where each element is a cell name that appears in the fragment file and the name of each element is the name of the cell in the Seurat object.
region	A genomic region, specified as a string in the format 'chr:start-end'. Can be a vector of regions.
tabix.file	A TabixFile object.
cells	Cells to include. Default is all cells present in the object.
verbose	Display messages
...	Additional arguments passed to StringToGRanges

Value

Returns a data frame

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