chainNetSyntenic: chainNetSyntenic

In ge11232002/CNEr: CNE Detection and Visualization

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)

ge11232002/CNEr documentation built on Oct. 26, 2022, 7:08 p.m.