CNE-class {CNEr} | R Documentation

## Class `"CNE"`

### Description

`CNE` class contains all the meta-data of CNEs, including the pair of assemblies, the thresholds, the intermediate and final CNE sets.

### Usage

    ### Constructors:
    CNE(assembly1Fn=character(1), assembly2Fn=character(1),
        axt12Fn=character(), axt21Fn=character(),
        window=50L, identity=50L,
        CNE12=GRangePairs(), CNE21=GRangePairs(),
        CNEMerged=GRangePairs(), CNEFinal=GRangePairs(),
        aligner="blat", cutoffs1=4L, cutoffs2=4L)

    ### Accessor-like methods:
    ## S4 method for signature 'CNE'
    thresholds(x)
    ## S4 method for signature 'CNE'
    CNE12(x)
    ## S4 method for signature 'CNE'
    CNE21(x)
    ## S4 method for signature 'CNE'
    CNEMerged(x)
    ## S4 method for signature 'CNE'
    CNEFinal(x)

    ## ... and more (see Methods)

### Arguments

`assembly1Fn,assembly2Fn` | Object of class `"character"`: The twoBit filenames of assembly1, assembly2
`axt12Fn,axt21Fn` | Object of class `"character"`: The Axt filenames of assembly1 to assembly2, assembly2 to assembly1
`window` | Object of class `"integer"`: The window size for scanning CNEs. By default, it is 50.
`identity` | Object of class `"integer"`: The identity over the window size for scanning CNEs. By default, it is 50.
`CNE12` | Object of class `"GRangePairs"`: The preliminary CNEs from axt file with assembly1 as reference.
`CNE21` | Object of class `"GRangePairs"`: The preliminary CNEs from axt file with assembly2 as reference.
`CNEMerged` | Object of class `"GRangePairs"`: The CNEs after merging CNE1 and CNE2.
`CNEFinal` | Object of class `"GRangePairs"`: The CNEs after being realigned back to reference genome, with blat in current implementation.
`aligner` | Object of class `"character"`: The method to realign CNEs back to the reference genome.
`cutoffs1, cutoffs2` | Object of class `"integer"`: The CNEs with more than the cutoff hits on the reference genome are removed.
`x` | Object of class `"CNE"`: A `"CNE"` object.

### Methods

CNE12

  `signature(x = "CNE")`: Get the CNE1 results.

CNE21

  `signature(x = "CNE")`: Get the CNE2 results.

CNEMerged

  `signature(x = "CNE")`: Get the merged CNE results.

CNEFinal

  `signature(x = "CNE")`: Get the final CNE results.

thresholds

  `signature(x = "CNE")`: Get the thresholds used for scanning CNEs.

### Author(s)

Ge Tan

### Examples

      library(GenomicRanges)
      ## Constructor
      CNE12 <- GRangePairs(first=GRanges(seqnames=c("chr13", "chr4", "chr4"),
                                         ranges=IRanges(start=c(71727138,150679343,
                                                                146653164),
                                                        end=c(71727224, 150679400,
                                                              146653221)),
                                         strand="+"),
                           second=GRanges(seqnames=c("chr1"),
                                          ranges=IRanges(start=c(29854162, 23432387,
                                                                 35711077),
                                                         end=c(29854248, 23432444,
                                                               35711134)),
                                          strand="+")
                           )
      CNE21 <- GRangePairs(first=GRanges(seqnames=c("chr1"),
                                        ranges=IRanges(start=c(29854162, 23432387,
                                                               35711077),
                                                       end=c(29854248, 23432444,
                                                             35711134)),
                                        strand="+"),
                           second=GRanges(seqnames=c("chr13", "chr4", "chr4"),
                                          ranges=IRanges(start=c(71727138,150679343,
                                                                 146653164),
                                                         end=c(71727224, 150679400,
                                                               146653221)),
                                          strand="+")
                           )
      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=50L,
                 CNE12=CNE12, CNE21=CNE21, CNEMerged=CNE12, CNEFinal=CNE12,
                 aligner="blat", cutoffs1=4L, cutoffs2=4L)

      ## Accessor
      CNE12(cne)
      CNE21(cne)
      thresholds(cne)
      CNEMerged(cne)
      CNEFinal(cne)

[Package CNEr version 1.20.0 Index]