netToAxt: netToAxt

In CNEr: CNE Detection and Visualization

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)

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.