axtChain {CNEr} | R Documentation

## axtChain

### Description

Wrapper function of `axtChain`: chain together psl alignments. If two matching alignments next to each other are close enough, they are joined into one segment. This function doesn't work on Windows platform since Kent utilities only support Unix-based platforms.

### Usage

      axtChain(psls, chains=sub("\\.psl$", ".chain", psls, ignore.case=TRUE),
               assemblyTarget, assemblyQuery,
               distance=c("far", "medium", "near"),
               removePsl=TRUE, binary="axtChain")

### Arguments

`psls` | `character`(n): file names of input psl files.
`chains` | `character`(n): file names of output chain files. By default, in the same folder of input lav files with same names.
`assemblyTarget` | `character`(1): the file name of target assembly twoBit file.
`assemblyQuery` | `character`(1): the file name of query assembly twoBit file.
`distance` | It can be "far", "medium" or "close". It decides the score matrix used in lastz aligner. See '?scoringMatrix' for more details.
`removePsl` | `boolean`: When `TRUE`, the input psl files will be removed from the conversion.
`binary` | `character`(1): the name/filename of the binary `axtChain` to call.

### Value

`character`(n): the file names of output chain files.

### Author(s)

Ge Tan

### References

http://hgdownload.cse.ucsc.edu/admin/exe/

### See Also

`lavToPsl`

### Examples

      ## Not run:
      ## This example doesn't run because it requires two bit files and external
      ## Kent utilities.
        psls <- tools::list_files_with_exts(
                  dir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt", exts="psl")
        assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
        assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
        axtChain(psls, assemblyTarget=assemblyTarget,
                 assemblyQuery=assemblyQuery, distance="far",
                 removePsl=FALSE, binary="axtChain")

    ## End(Not run)

[Package CNEr version 1.20.0 Index]