blatCNE: Wrapper function of blat for 'CNE' object

In ge11232002/CNEr: CNE Detection and Visualization

Wrapper function of blat for CNE object

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)

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