scoringMatrix: scoringMatrix

In CNEr: CNE Detection and Visualization

Description

Generates the scoring matrix for lastz aligner.

Usage

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

Arguments

distance

It can be "far", "medium" or "close". It defines the scoring matrix used in lastz aligner. Generally, if two species are close to each other, for example human and chimp, "close" should be used. If two species have a divergence time of 100 MYA, "far" should be used. In other cases, "medium" should be used.

Value

A matrix of the scoring matrix is returned.

Note

HOXD70 is medium. HoxD55 is far. human-chimp.v2 is close.

Author(s)

Ge Tan

References

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

See Also

lastz

Examples

  scoringMatrix(distance="far")

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.