Methods for GRanges objects
findOverlaps(query, subject, ...):
Find the feature indices in
subject that overlap the
genomic intervals in
query is a
GRanges object and subject is a
Additional arguments to the
findOverlaps method in the
package IRanges can be passed through the
object is an instance of the
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.
numberProbes are convenient accessors for these
Accessor for the UCSC genome build.
Integer vector indicating the number of probes (markers) for each
object. Equivalent to
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
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)
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