lastz {CNEr} | R Documentation

## lastz wrapper

### Description

Wrapper function of `lastz` to do the pairwise whole genome alignment. This function doesn't work on Windows platform.

### Usage

      lastz(assemblyTarget, assemblyQuery, outputDir = ".",
            chrsTarget = NULL, chrsQuery = NULL,
            distance = c("far", "medium", "near"), binary = "lastz",
            mc.cores = getOption("mc.cores", 2L), echoCommand = FALSE)

### Arguments

`assemblyTarget` | `character`(1): the file name of target assembly twoBit file.
`assemblyQuery` | `character`(1): the file name of query assembly twoBit file.
`outputDir` | `character`(1): the folder to put the generated lav files.
`chrsTarget` | NULL or `character`(n): when it's NULL, all the available chromosomes from the target assembly will be aligned.
`chrsQuery` | NULL or `character`(n): when it's NULL, all the available chromosomes from the query assembly will be aligned.
`distance` | It can be "far", "medium" or "near". It decides the score matrix used in lastz aligner. See '?scoringMatrix' for more details.
`binary` | `character`(1): the name/filename of the binary `lastz` to call.
`mc.cores` | `integer`(1): the number of threads to use. By default, `getOption("mc.cores", 2L)`.
`echoCommand` | `boolean`(1): When `TRUE`, only the command to run `lastz` is returned.

### Value

A `character`(n) vector of ouput lav file names.

### Note

`lastz` aligner must be installed on the machine to use this function.

### Author(s)

Ge Tan

### References

http://www.bx.psu.edu/~rsharris/lastz/

### See Also

`lavToPsl`

### Examples

      ## Not run:
      ## This example doesn't run because it requires two bit files and external
      ## Kent utilities.
        assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
        assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
        lavs <- lastz(assemblyTarget, assemblyQuery,
                      outputDir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
    			            chrsTarget=c("chr1", "chr2", "chr3"),
    			            chrsQuery=c("chr1", "chr2", "chr3"),
    			            distance="far", mc.cores=4)

    ## End(Not run)

[Package CNEr version 1.22.0 Index]