getPeakSet.snakeATAC

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

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

Value

GRanges object containing consensus peak set

Author

Fabian Mueller