lastz: lastz wrapper

In ge11232002/CNEr: CNE Detection and Visualization

lastz wrapper

Description

Wrapper function of lastz to do the pairwise whole genome alignment. This function doesn't work on Windows platform.

Usage

  lastz(assemblyTarget, assemblyQuery, outputDir = ".",
        chrsTarget = NULL, chrsQuery = NULL,
        distance = c("far", "medium", "near"), binary = "lastz", 
        mc.cores = getOption("mc.cores", 2L), echoCommand = FALSE)

Arguments

assemblyTarget	character(1): the file name of target assembly twoBit file.
assemblyQuery	character(1): the file name of query assembly twoBit file.
outputDir	character(1): the folder to put the generated lav files.
chrsTarget	NULL or character(n): when it's NULL, all the available chromosomes from the target assembly will be aligned.
chrsQuery	NULL or character(n): when it's NULL, all the available chromosomes from the query assembly will be aligned.
distance	It can be "far", "medium" or "near". It decides the score matrix used in lastz aligner. See '?scoringMatrix' for more details.
binary	character(1): the name/filename of the binary lastz to call.
mc.cores	integer(1): the number of threads to use. By default, getOption("mc.cores", 2L).
echoCommand	boolean(1): When TRUE, only the command to run lastz is returned.

Value

A character(n) vector of ouput lav file names.

Note

lastz aligner must be installed on the machine to use this function.

Author(s)

Ge Tan

References

http://www.bx.psu.edu/~rsharris/lastz/

See Also

lavToPsl

Examples

  ## Not run: 
  ## This example doesn't run because it requires two bit files and external
  ## Kent utilities.
    assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
    assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
    lavs <- lastz(assemblyTarget, assemblyQuery, 
                  outputDir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
			            chrsTarget=c("chr1", "chr2", "chr3"),
			            chrsQuery=c("chr1", "chr2", "chr3"),
			            distance="far", mc.cores=4)
  
## End(Not run)

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