blatCNE {CNEr} | R Documentation

## 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)

[Package CNEr version 1.30.0 Index]