findOverlapsBench: Find occuring GRanges overlapping with the benchmarking set...

In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference

Description

Find occuring GRanges overlapping with the benchmarking set (positive + negative examples)

Usage

findOverlapsBench(occuring, benchmarking, predictor_col = "Sig",
  labels_col = "for_benchmarking", normalise = T,
  select_predictor_per_range = min, ...)

Arguments

occuring	GRanges object, occuring feature instances
benchmarking	GRanges object, feature instances for benchmarking
predictor_col	name of the metadata column in occuring that contains 1 - predictor value (such as p-value)
labels_col	name of the metadata column in benchmarking that contains labels for benchmarking (for, example 0 for negative and 1 for positive)
normalise	logical, normalise predictor value, just in case predictor doesn't span the full range between 0 ... 1
...	arguments such as maxgap, minoverlap passed to findOverlaps

Value

Genomic Ranges list object containing N randomised GRanges objects

Author(s)

Vitalii Kleshchevnikov

See Also

ELMdb2GRanges, GRangesINinteractionSubsetFASTA

vitkl/SLIMFinderR documentation built on May 3, 2019, 8:08 p.m.