make.unique.psl: Convert a PSL alignment data.frame into a minimal 1:1...

In drmjc/blat: Import/Export functions for UCSC genome BLAT alignments

Description

Convert a PSL alignment data.frame into a minimal 1:1 alignment file where each query has at most one target

Usage

  make.unique.psl(psl, quick = FALSE, ambig.thresh = 0.95)

Arguments

psl	a psl data.frame; see import.psl
quick	if TRUE, then only the best hit for each transcript is returned with no regard for ties. If there is a score tie for a transcript then the first one (alphabetically) will be returned.
ambig.thresh	undocumented

Value

a data.frame with 1 row per query containing the best alignment for each query.

Ambiguity Rules

If there's only one alignment for a query, then no change If there's > 1 alignment for a query, work out the pslScore's for each alignment, and choose the best one. If there is a tie for the best alignment, then the one closest to the top of the data.frame is chosen. In the case of a tie, warning messages are displaying indicating to the user whether the ties were all on the same chromosome or not.

Author(s)

Mark Cowley, 12 April 2006

Examples

f <- file.path(system.file(package="blat"), "examples", "test.psl")
psl <- import.psl(f, score=FALSE)
make.unique.psl(psl)

drmjc/blat documentation built on May 15, 2019, 2:22 p.m.