DsATAC.fragmentBed: DsATAC.fragmentBed

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

DsATAC.fragmentBed

Description

Create a DsATAC dataset from multiple input fragment bed files

Usage

DsATAC.fragmentBed(
  sampleAnnot,
  bedFiles,
  genome,
  regionSets = NULL,
  sampleIdCol = NULL,
  diskDump = FALSE,
  keepInsertionInfo = TRUE
)

Arguments

sampleAnnot	data.frame specifying the sample annotation table
bedFiles	either a character vector of the same length as sampleAnnot has rows, specifying the file paths of the bed files for each sample or a single character string specifying the column name in sampleAnnot where the file paths can be found
genome	genome assembly
regionSets	a list of GRanges objects which contain region sets over which count data will be aggregated
sampleIdCol	column name in the sample annotation table containing unique sample identifiers. If NULL (default), the function will look for a column that contains the word "sample"
diskDump	should large data objects (count matrices, fragment data, ...) be disk-backed to save main memory
keepInsertionInfo	flag indicating whether to maintain the insertion information in the resulting object. Only relevant when type=="insBam".

Value

DsATAC object

Author(s)

Fabian Mueller

GreenleafLab/ChrAccR documentation built on March 22, 2023, 11:42 p.m.