chainMergeSort {CNEr} | R Documentation

## chainMergeSort

### Description

Wrapper function of `chainMergeSort`: Combines sorted files into a larger sorted file. This function doesn't work on Windows platform since Kent utilities only support Linux and Unix platforms.

### Usage

      chainMergeSort(chains, assemblyTarget, assemblyQuery,
                     allChain=paste0(sub("\\.2bit$", "", basename(assemblyTarget),
                                        ignore.case=TRUE), ".",
                                     sub("\\.2bit$", "", basename(assemblyQuery),
                                         ignore.case=TRUE), ".all.chain"),
                     removeChains=TRUE, binary="chainMergeSort")

### Arguments

`chains` | `character`(n): file names of input chains files.
`assemblyTarget` | `character`(1): the file name of target assembly twoBit file.
`assemblyQuery` | `character`(1): the file name of query assembly twoBit file.
`allChain` | `character`(1): file names of merged allChain file.
`removeChains` | `boolean`: When `TRUE`, the input chains files will be removed after the conversion.
`binary` | `character`(1): the name/filename of the binary `chainMergeSort` to call.

### Details

This allChain file is what we get from UCSC download, e.g., hg19.danRer7.all.chain.gz.

### Value

`character`(1): the file names of merged allChain file.

### Author(s)

Ge Tan

### References

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

### See Also

`axtChain`

### Examples

      ## Not run:
      ## This example doesn't run because it requires two bit files and external
      ## Kent utilities.
        chains <- tools::list_files_with_exts(
                    dir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt", exts="chain")
        assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
        assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
        chainMergeSort(chains, assemblyTarget, assemblyQuery,
          allChain=file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
                             paste0(sub("\\.2bit$", "", basename(assemblyTarget),
                                        ignore.case=TRUE), ".",
                                    sub("\\.2bit$", "", basename(assemblyQuery),
                                        ignore.case=TRUE), ".all.chain")),
          removeChains=FALSE, binary="chainMergeSort")

    ## End(Not run)

[Package CNEr version 1.18.1 Index]