blatCNE: Wrapper function of blat for 'CNE' object

In CNEr: CNE Detection and Visualization

Description

This wrapper function blat the CNEs against the reference genome. Note that blat must be installed on your system.

Usage

  blatCNE(cne, blatOptions=NULL, cutIdentity=90)

Arguments

cne	cne object after cneMerge step.
blatOptions	character(1): the blat options. When it is NULL, the options will be chosen based on the window size for scanning CNEs.
cutIdentity	integer(1): the minimum sequence identity (in percent) for a match in blat. By default, it is 90.

Details

When winSize > 45, the blat option is "-tileSize=11 -minScore=30 -repMatch=1024".

When 35 < winSize <= 45, the blat option is "-tileSize=10 -minScore=28 -repMatch=4096".

When the winSize <= 35, the blat option is "-tileSize=9 -minScore=24 -repMatch=16384".

Value

A CNE object with a final set of CNEs.

Author(s)

Ge Tan

Examples

  ## Not run: 
    data(CNEDanRer10Hg38)
    data(CNEHg38DanRer10)
    cne <- CNE(assembly1Fn=file.path(system.file("extdata",
                                    package="BSgenome.Drerio.UCSC.danRer10"),
                        "single_sequences.2bit"),
               assembly2Fn=file.path(system.file("extdata",
                                    package="BSgenome.Hsapiens.UCSC.hg38"),
                        "single_sequences.2bit"),
               window=50L, identity=45L, CNE12=CNEDanRer10Hg38[["45_50"]],
               CNE21=CNEHg38DanRer10[["45_50"]], aligner="blat")
    cne <- cneMerge(cne)
    cne <- blatCNE(cne)
  
## End(Not run)

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