getConsensusPeakSet

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
)

Arguments

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

Value

GRanges object the containing consensus peak set

Author

Fabian Mueller