axtChain: axtChain

In CNEr: CNE Detection and Visualization

Description

Wrapper function of axtChain: chain together psl alignments. If two matching alignments next to each other are close enough, they are joined into one segment. This function doesn't work on Windows platform since Kent utilities only support Unix-based platforms.

Usage

  axtChain(psls, chains=sub("\\.psl$", ".chain", psls, ignore.case=TRUE),
           assemblyTarget, assemblyQuery,
           distance=c("far", "medium", "near"),
           removePsl=TRUE, binary="axtChain")

Arguments

psls	character(n): file names of input psl files.
chains	character(n): file names of output chain files. By default, in the same folder of input lav files with same names.
assemblyTarget	character(1): the file name of target assembly twoBit file.
assemblyQuery	character(1): the file name of query assembly twoBit file.
distance	It can be "far", "medium" or "close". It decides the score matrix used in lastz aligner. See '?scoringMatrix' for more details.
removePsl	boolean: When TRUE, the input psl files will be removed from the conversion.
binary	character(1): the name/filename of the binary axtChain to call.

Value

character(n): the file names of output chain files.

Author(s)

Ge Tan

References

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

See Also

lavToPsl

Examples

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

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