chainNetSyntenic {CNEr} | R Documentation

## chainNetSyntenic

### Description

Wrapper function of chainNetSyntenic: Makes alignment nets out of chains and adds synteny info to net. This function doesn't work on Windows platform since Kent utilities only support Linux and Unix platforms.

### Usage

      chainNetSyntenic(allPreChain, assemblyTarget, assemblyQuery,
                       netSyntenicFile=paste0(sub("\\.2bit$", "",
                                                  basename(assemblyTarget),
                                                  ignore.case = TRUE), ".",
                                              sub("\\.2bit$", "",
                                                  basename(assemblyQuery),
                                                  ignore.case = TRUE),
                                                  ".noClass.net"),
                       binaryChainNet="chainNet", binaryNetSyntenic="netSyntenic")

### Arguments

`allPreChain` | `character`(1): file names of input allPreChain file.
`assemblyTarget` | `character`(1): the file name of target assembly twoBit file.
`assemblyQuery` | `character`(1): the file name of query assembly twoBit file.
`netSyntenicFile` | `character`(1): file names of output netSyntenicFile file.
`binaryChainNet` | `character`(1): the name/filename of the binary `chainNet` to call.
`binaryNetSyntenic` | `character`(1): the name/filename of the binary `netSyntenic` to call.

### Details

Add classification information using the database tables: actually this step is not necessary in this pipeline according to http://blog.gmane.org/gmane.science.biology.ucscgenome.general/month=20130301. The class information will only be used for Genome Browser. Since it needs some specific modification of the table names for certain species, we skip this step now. If this step is done, then the generated class.net is the gzipped net file that you see in UCSC Downloads area.

### Value

`character`(1): the file names of generated net file.

### Author(s)

Ge Tan

### References

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

### See Also

`chainPreNet`

### Examples

      ## Not run:
      ## This example doesn't run because it requires two bit files and external
      ## Kent utilities.
        allPreChain <- 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"
        chainNetSyntenic(allPreChain, assemblyTarget, assemblyQuery,
                         netSyntenicFile=file.path(
                           "/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
                                                   paste0(sub("\\.2bit$", "",
                                                          basename(assemblyTarget),
                                                          ignore.case = TRUE), ".",
                                                          sub("\\.2bit$", "",
                                                          basename(assemblyQuery),
                                                          ignore.case = TRUE),
                                                  ".noClass.net")),
                         binaryChainNet="chainNet", binaryNetSyntenic="netSyntenic")

    ## End(Not run)

[Package CNEr version 1.20.0 Index]