scoringMatrix {CNEr} | R Documentation

## scoringMatrix

### 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")

[Package CNEr version 1.20.0 Index]