CNE-class: Class '"CNE"'

In CNEr: CNE Detection and Visualization

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)

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