gUnique: gUnique

In mskilab/gChain: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

gUnique

Description

remove duplicate x to y mappings

Will select only the longest, and most "leftward" in genomic coordaintes (in that order) entry of each unique x to y pair, where uniqueness is determined by seqnames and strand, but not by position. This could occur, for instance, if a read has multiple mappings to a genomic contig or multiple mappings within one chromosome. Occasionally, one might want to take only the longest match, and discard secondary alignments.

Usage

gUnique(gc)

Arguments

gc	gChain object to deduplicate

Value

Deduplicated gChain

Note

This is a bit of a hack, as there are better ways to remove dupes before this step

mskilab/gChain documentation built on Sept. 28, 2022, 3:45 p.m.