chainPreNet {CNEr} | R Documentation

## chainPreNet

### Description

Wrapper function of `chainPreNet`: Removes chains that don't have a chance of being netted. This function doesn't work on Windows platform since Kent utilities only support Linux and Unix platforms.

### Usage

      chainPreNet(allChain, assemblyTarget, assemblyQuery,
                  allPreChain=paste0(sub("\\.2bit$", "", basename(assemblyTarget),
                                         ignore.case = TRUE), ".",
                                     sub("\\.2bit$", "", basename(assemblyQuery),
                                         ignore.case = TRUE), ".all.pre.chain"),
                  removeAllChain=TRUE, binary="chainPreNet")

### Arguments

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

### Value

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

### Author(s)

Ge Tan

### References

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

### See Also

`chainMergeSort`

### Examples

      ## Not run:
      ## This example doesn't run because it requires two bit files and external
      ## Kent utilities.
        allChain <- file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
                              "danRer10.hg38.all.chain")
        assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
        assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
        chainPreNet(allChain, assemblyTarget, assemblyQuery,
                    allPreChain=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.pre.chain")),
                    removeAllChain=FALSE, binary="chainPreNet")

    ## End(Not run)

[Package CNEr version 1.22.0 Index]