greedy_algorithm: Greedy algorithm for a set of overlapping intervals.
In robbueck/wisard: Perform wighted interval scheduling on a Genomic Ranges object

Description Usage Arguments Details Value See Also

View source: R/greedy.R

A function to create a set of non-overlapping intervals using a greedy algorithm by prefering intervals with higeher scores.

greedy_algorithm(
  granges_list,
  max_score = "raw_score",
  overlap = 0,
  is_circular = F,
  overhang = 0,
  use_strand = T,
  second_range = NULL
)

`granges_list`	A set of intervals as a GRangesList object. Requires a score column to be specified in `max_score`.
`max_score`	Name of a column in `granges_list` containing integers or floats to be used as a score to maximize over.
`overlap`	A non-negative integer specifying the allowed overlap between two intervals.
`is_circular`	Boolean. If set true, intervals are assumed to be on a circular scale.
`overhang`	A non-negative integer how much of the end is overlapping with the start. specifying for a linearized circular scale Ignored if is_circular is FALSE.
`use_strand`	Boolean. If TRUE, strand information is used to detect overlaps
`second_range`	Optional, name of a column in granges_list containing another GRangesList object. If set, for intervals in granges_list to be compatible, they also have to be compatible in second_range.

The algorithm seeks to maximize the sum of a score given in max_score, but does not necessarily return the best possible solution. Created mainly for comparison with the WIS-algorithm function get_wis.

When is_circular is TRUE, intervals exceeding the end of the scale given by (seqlength(granges_list) - overhang) are wrapped to the beginning.

A GRangesList object with intervals compatible according to the specified options.

https://doi.org/10.1093/bioinformatics/bth324 for description of the algorithm

robbueck/wisard documentation built on Jan. 25, 2022, 12:35 a.m.