GRanges-methods {oligoClasses} | R Documentation

## Methods for GRanges objects

### Description

Methods for GRanges objects

### findOverlaps methods

  `findOverlaps(query, subject, ...)`:

  Find the feature indices in `subject` that overlap the genomic intervals in `query`, where `query` is a `GRanges` object and subject is a `gSet`-derived object. Additional arguments to the `findOverlaps` method in the package IRanges can be passed through the `...` operator.

### Accessors

`object` is an instance of the `GRanges` class.

  `coverage2(object)`:

  For the `GRanges` and `GRangesList` objects returned by the hidden Markov model implemented in the "VanillaICE" package and the segmentation algorithm in the "MinimumDistance" package, the intervals are annotated by the number of probes (markers) for SNPs and nonpolymorphic regions. `coverage2` and `numberProbes` are convenient accessors for these annotations.

  `genomeBuild(object)`:

  Accessor for the UCSC genome build.

  `numberProbes(object)`:

  Integer vector indicating the number of probes (markers) for each range in `object`. Equivalent to `coverage2`.

  `state(object)`:

  Accessor for the `elementMetadata` column 'state', when applicable. State is used to contain the index of the inferred copy number state for various `hmm` methods defined in the VanillaICE.

### See Also

`GRanges`

### Examples

    	  library(IRanges)
    	  library(GenomicRanges)
    	  gr1 <- GRanges(seqnames = "chr2", ranges = IRanges(3, 6),
    			 state=3L, numberProbes=100L)
    	  ## convenience functions
    	  state(gr1)
    	  numberProbes(gr1)

    	  gr2 <- GRanges(seqnames = c("chr1", "chr1"),
    			 ranges = IRanges(c(7,13), width = 3),
    			 state=c(2L, 2L), numberProbes=c(200L, 250L))
    	  gr3 <- GRanges(seqnames = c("chr1", "chr2"),
    			 ranges = IRanges(c(1, 4), c(3, 9)),
    			 state=c(1L, 4L), numberProbes=c(300L, 350L))
    	  ## Ranges organized by sample
    	  grl <- GRangesList("sample1" = gr1, "sample2" = gr2, "sample3" = gr3)
    	  sampleNames(grl) ## same as names(grl)
    	  numberProbes(grl)
    	  chromosome(grl)
    	  state(grl)
    	  gr <- stack(grl)
    	  sampleNames(gr)
    	  chromosome(gr)
    	  state(gr)

[Package oligoClasses version 1.48.0 Index]