axtChain: axtChain

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 fragment. This function doesn't work on Windows platform since Kent utilities only support Linux and Unix platform.

Usage

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

References

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

Examples

Run this code

  ## 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)