get_best_start: Get best start for WIS

In robbueck/wisard: Perform wighted interval scheduling on a Genomic Ranges object

Description

For a circular scale, this function finds the best interval(s) to start the WIS alsogrithm with.

Usage

get_best_start(granges_list, overhang = 0)

Arguments

granges_list	A GRangesList object containing the intervals.
overhang	A non-negative integer specifying for a linearized circular scale how much of the end is overlapping with the start.

Details

Takes a circular GRangesList object and finds the best intervals to start with. Ideally, this is an inverval, whose start position is not overlapped by any other interval. If no such interval exists, the interval with the least overlaps at its start position and each interval overlapping this position are returned.

Strand information is ignored here, has to be taken into account before calling this fucntion.

Also checks if overhang is long enough or should be extended, e.g. in BLAST-searches by copying a longer sequence from the beginning to the end.

Value

Returns the index of the optimal interval to start a WIS-algorithm with. If no such interval exists, returns an integer vector with indices for the best possible interval and all intervalls overlapping its starting position.

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