CNEr (version 1.8.3)

chainMergeSort: chainMergeSort

Description

Wrapper function of chainMergeSort: Combine sorted files into larger sorted file. This function doesn't work on Windows platform since Kent utilities only support Linux and Unix platform.

Usage

chainMergeSort(chains, assemblyTarget, assemblyQuery, allChain=paste0(sub("\\.2bit$", "", basename(assemblyTarget), ignore.case=TRUE), ".",  sub("\\.2bit$", "", basename(assemblyQuery),  ignore.case=TRUE), ".all.chain"), removeChains=TRUE, binary="chainMergeSort")

Arguments

chains

character(n): file names of input chains files.

assemblyTarget

character(1): the file name of target assembly twoBit file.

assemblyQuery

character(1): the file name of query assembly twoBit file.

allChain

character(1): file names of merged allChain file.

removeChains

boolean: When TRUE, the input chains files will be removed after the conversion.

binary

character(1): the name/filename of the binary chainMergeSort to call.

Value

character(1): the file names of merged allChain file.

Details

This allChain file is what we get from UCSC download, e.g., hg19.danRer7.all.chain.gz.

References

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

See Also

axtChain

Examples

  ## Not run: 
#   ## This example doesn't run because it requires two bit files and external
#   ## Kent utilities.
#     chains <- tools::list_files_with_exts(
#                 dir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt", exts="chain")
#     assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
#     assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
#     chainMergeSort(chains, assemblyTarget, assemblyQuery,
#       allChain=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.chain")),
#       removeChains=FALSE, binary="chainMergeSort")
#   ## End(Not run)