DsATAC.cellranger: DsATAC.cellranger

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

DsATAC.cellranger

Description

Create a DsATAC dataset from multiple input files output by 10x cellranger

Usage

DsATAC.cellranger(
  sampleAnnot,
  sampleDirPrefixCol,
  genome,
  dataDir = "",
  regionSets = NULL,
  addPeakRegions = TRUE,
  sampleIdCol = sampleDirPrefixCol,
  keepInsertionInfo = FALSE,
  diskDump.fragments = keepInsertionInfo
)

Arguments

sampleAnnot	data.frame specifying the sample annotation table
sampleDirPrefixCol	column name specifying the directory prefix for each sample in the sample annotation table
genome	genome assembly
dataDir	directory where the files are located
regionSets	a list of GRanges objects which contain region sets over which count data will be aggregated
addPeakRegions	should a merged set of peaks be created as one of the region sets (merged, non-overlapping peaks of width=500bp from the peaks of individual samples)
sampleIdCol	column name or index in the sample annotation table containing unique sample identifiers
keepInsertionInfo	flag indicating whether to maintain the insertion information in the resulting object.
diskDump.fragments	Keep fragment coordinates stored on disk rather than in main memory. This saves memory, but increases runtime and I/O.

Value

DsATAC object

Author(s)

Fabian Mueller

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