DsATAC.snakeATAC: DsATAC.snakeATAC
In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

DsATAC.snakeATAC

R Documentation

DsATAC.snakeATAC

Description

Create a DsATAC dataset from multiple input files output by snakeATAC

Usage

DsATAC.snakeATAC(
  sampleAnnot,
  filePrefixCol,
  genome,
  dataDir = "",
  regionSets = NULL,
  sampleIdCol = filePrefixCol,
  type = "insBam",
  diskDump = FALSE,
  keepInsertionInfo = TRUE,
  bySample = FALSE,
  pairedEnd = TRUE
)

Arguments

`sampleAnnot`	data.frame specifying the sample annotation table
`filePrefixCol`	column name specifying the file prefix for each sample in the sample annotation table. If `dataDir` is not empty (i.e. not `""`) filenames are assumed to be relative to that directory and a corresponding filename suffix will be appended
`genome`	genome assembly
`dataDir`	directory where the files are located. If it is the empty character (`""`; default) it is assumed that `filePrefixCol` specifies the full path to the input files
`regionSets`	a list of GRanges objects which contain region sets over which count data will be aggregated
`sampleIdCol`	column name or index in the sample annotation table containing unique sample identifiers
`type`	input data type. Currently only "insBed" (insertion beds), "insBam" (insertion info inferred from bam files (aligned reads); default) and "bam" (aligned reads) are supported
`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"`.
`bySample`	process sample-by-sample to save memory (currently only has an effect for `type=="insBam"`)
`pairedEnd`	is the input data paired-end? Only relevant when `type=="insBam"`.