CNE merge function

Description

Removes the CNEs which overlap on both genomes.

Usage

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  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

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  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)

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