cneMerge-methods {CNEr} | R Documentation

## CNE merge function

### Description

Removes the CNEs which overlap on both genomes.

### Usage

      cneMerge(cne12, cne21)

### Arguments

`cne12` | A object of `CNE` or `GRangePairs`.
`cne21` | A object of `GRangePairs` object. When cne12 is a `CNE` object, cne21 can be missing.

### Value

A `GRangePairs` of CNEs or a `CNE` object is returned. In this table, the order of columns is consistent with cne1. For instance, if cne1 has the first three columns for zebrafish and next three columns for human, in the merged table, the first three columns are still the coordinates for zebrafish while the next three columns are the coordinates for human.

### Author(s)

Ge Tan

### Examples

      library(GenomicRanges)
      firstGRange <- GRanges(seqnames=c("chr1", "chr1", "chr2", "chr2", "chr5"),
                             ranges=IRanges(start=c(1, 20, 2, 3, 1),
                                            end=c(10, 25, 10, 10, 10)),
                             strand="+")
      lastGRange <- GRanges(seqnames=c("chr15", "chr10", "chr10", "chr10", "chr15"),
                            ranges=IRanges(start=c(1, 25, 50, 51, 5),
                                           end=c(8, 40, 55, 60, 10)),
                            strand="+")
      cne12 <- GRangePairs(firstGRange[1:3], lastGRange[1:3])
      cne21 <- GRangePairs(lastGRange[4:5], firstGRange[4:5])

      ## GRangePairs, GRangePairs
      cneMerge(cne12, cne21)

      ## CNE, missing
      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, aligner="blat")
      cneMerge(cne)

[Package CNEr version 1.20.0 Index]