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

getPeakSet.snakeATAC

R Documentation

getPeakSet.snakeATAC

Description

Retrieve a consensus set of ATAC peaks from the snakeATAC pipline run

Usage

getPeakSet.snakeATAC(
  sampleAnnot,
  filePrefixCol,
  genome,
  dataDir,
  sampleIdCol = filePrefixCol,
  type = "summits_no_fw",
  unifWidth = 500L,
  replicateCol = NA,
  replicatePercReq = 1,
  replicateConsSelect = FALSE,
  keepOvInfo = FALSE
)

Arguments

`sampleAnnot`	data.frame specifying the sample annotation table
`filePrefixCol`	column name specifying the file prefix for each sample in the sample annotation table
`genome`	genome assembly
`dataDir`	directory where the files are located
`sampleIdCol`	column name or index in the sample annotation table containing unique sample identifiers
`type`	input data type. Currently only "summits_no_fw" (non-overlapping, fixed-width peaks deduced from summits)
`unifWidth`	width of the peaks if the results have uniform peak lengths
`replicateCol`	column name specifying the replicate group for cross-checking coverage across replicates
`replicatePercReq`	percentile of replicates in a group required to contain a peak in order to keep it. E.g. a value of 1 (default) means that all replicates in a group are required to contain that peak in order to keep it.
`replicateConsSelect`	if set, the peak set will also be checked for consistency, i.e. in order to retain a peak it has to be consistently be present or absent in each replicate group (as specified in `replicatePercReq` percent of samples)
`keepOvInfo`	keep annotation columns in the elementMetadata of the results specifying whether a consensus peak overlaps with a peak in each sample