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 )
GRangesList object containing the peak sets for each sample
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.
vector of group memberships (numeric, character or factor). must be of the same length as
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.
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)
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
keep annotation columns in the elementMetadata of the results specifying whether a consensus peak overlaps with a peak in each sample
GRanges object the containing consensus peak set