chainPreNet: chainPreNet

In CNEr: CNE Detection and Visualization

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)

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