getConsensusPeakSet: getConsensusPeakSet
In demuellae/ChrAccR: Analyzing chromatin accessibility data in R

Description Usage Arguments Value Author(s)

Retrieve a consensus peak set from a set of peak lists

getConsensusPeakSet(
  grl,
  mode = "no_by_score",
  grouping = NULL,
  groupAgreePerc = 1,
  groupConsSelect = FALSE,
  scoreCol = "score",
  keepOvInfo = FALSE
)

`grl`	list or `GRangesList` object containing the peak sets for each sample
`mode`	consensus mode. Currently only "no_by_score" (non-overlapping; i.e. select the peak with the highest score from each set of overlapping peaks) is supported.
`grouping`	vector of group memberships (numeric, character or factor). must be of the same length as `grl`
`groupAgreePerc`	percentile of members 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.
`groupConsSelect`	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 group (as specified in `groupAgreePerc` percent of samples)
`scoreCol`	name of the column to be used as score in the `elementMetadata` of the peak sets. This will determine which peak is selected if multiple peaks overlap
`keepOvInfo`	keep annotation columns in the elementMetadata of the results specifying whether a consensus peak overlaps with a peak in each sample