netToAxt {CNEr} | R Documentation

## netToAxt

### Description

Wrapper function of `netToAxt` and `axtSort`: convert net (and chain) to axt, and sort axt files. This function doesn't work on the Windows platform since Kent utilities only support Linux and Unix platforms.

### Usage

      netToAxt(in.net, in.chain, assemblyTarget, assemblyQuery,
               axtFile=paste0(sub("\\.2bit$", "", basename(assemblyTarget),
                                  ignore.case = TRUE), ".",
                              sub("\\.2bit$", "", basename(assemblyQuery),
                                  ignore.case = TRUE), ".net.axt"),
               removeFiles=FALSE,
               binaryNetToAxt="netToAxt", binaryAxtSort="axtSort")

### Arguments

`in.net` | `character`(1): file names of input net file.
`in.chain` | `character`(1): file names of input chain file.
`assemblyTarget` | `character`(1): the file name of target assembly twoBit file.
`assemblyQuery` | `character`(1): the file name of query assembly twoBit file.
`axtFile` | `character`(1): file names of output axt file.
`removeFiles` | `boolean`: When `TRUE`, the input net and chain files will be removed after the conversion.
`binaryNetToAxt` | `character`(1): the name/filename of the binary `netToAxt` to call.
`binaryAxtSort` | `character`(1): the name/filename of the binary `axtSort` to call.

### Value

`character`(1): the file name of output axt file.

### Author(s)

Ge Tan

### References

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

### See Also

`chainNetSyntenic`

### Examples

      ## Not run:
        ## This example doesn't run because it requires two bit files and external
        ## Kent utilities.
        in.net <- file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
                            "danRer10.hg38.noClass.net")
        in.chain <- file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
                              "danRer10.hg38.all.pre.chain")
        assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
        assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
        netToAxt(in.net, in.chain, assemblyTarget, assemblyQuery,
                 axtFile=file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
                                   paste0(sub("\\.2bit$", "",
                                              basename(assemblyTarget),
                                              ignore.case = TRUE), ".",
                                          sub("\\.2bit$", "",
                                              basename(assemblyQuery),
                                              ignore.case = TRUE),
                                          ".net.axt")),
                 removeFiles=FALSE,
                 binaryNetToAxt="netToAxt", binaryAxtSort="axtSort")

    ## End(Not run)

[Package CNEr version 1.18.1 Index]