GRanges-methods: Methods for GRanges objects

In jmacdon/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

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)
  

jmacdon/oligoClasses documentation built on Aug. 11, 2020, 12:32 a.m.