CNEr (version 1.8.3)

scoringMatrix: scoringMatrix

Description

Generate the scoring matrix for lastz aligner.

Usage

scoringMatrix(distance = c("far", "medium", "close"))

Arguments

distance

It can be "far", "medium" or "close". It decides the score matrix used in lastz aligner. Generally, if two species are close to each other at human and chimp level, "close" should be used. If two species have a divergent time of 100 MYA, "far" should be used. In other cases, use "medium".

Value

A matrix of the scoring matrix is returned.

References

http://genomewiki.ucsc.edu/index.php/Hg38_17-way_conservation_lastz_parameters

See Also

lastz

Examples

  scoringMatrix(distance="far")