getConsensusPeakSet | R Documentation |
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 |
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 |
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 |
scoreCol |
name of the column to be used as score in the |
keepOvInfo |
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
Fabian Mueller
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