Question: GenomicRanges request - enable ignore.strand for findOverlaps comparing query with itself?
gravatar for Janet Young
5.3 years ago by
Janet Young730
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Janet Young730 wrote:
Hi there, I have a request for findOverlaps (GenomicRanges) - hopefully it's an easy one. Is it possible to implement the ignore.strand options for findOverlaps calls where we're comparing a query GRanges with itself? The reason I ask is that I'm looking through a set of genes to find pairs that overlap on opposite strands. Below is some code that should explain it (I'm using the devel packages). thanks very much, Janet ##### GRanges library(GenomicRanges) ## an example GRanges object, taken from the findOverlaps-methods {GenomicRanges} help page: gr <- GRanges(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), ranges = IRanges(1:10, width = 10:1, names = head(letters,10)), strand = Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)), score = 1:10, GC = seq(1, 0, length=10)) ## findOverlaps works, of course, finds 24 hits findOverlaps(gr) ## ignoreSelf and ignoreRedundant are useful: gives me just 7 useful pairs to explore more: findOverlaps(gr, ignoreSelf=TRUE, ignoreRedundant=TRUE) ## but I'm not getting hits for overlaps on opposite strands - I'd like to use ignore.strand, but it only works if we supply both query and subject. When I suppy gr as both query and subject, I get 34 pairs ignoring the strand: findOverlaps(gr, ignore.strand=TRUE) # Error in .local(query, subject, maxgap, minoverlap, type, select, ...) : # unused argument (ignore.strand = TRUE) findOverlaps(gr, gr, ignore.strand=TRUE) ## but now that I'm supplying the subject, I can't use the other two useful options (ignoreSelf and ignoreRedundant) that help me quickly get the pairs I'd like to explore more findOverlaps(gr, gr, ignore.strand=TRUE, ignoreSelf=TRUE, ignoreRedundant=TRUE) # Error in .local(query, subject, maxgap, minoverlap, type, select, ...) : # unused arguments (ignoreSelf = TRUE, ignoreRedundant = TRUE) sessionInfo() R version 3.1.0 Patched (2014-05-26 r65771) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicRanges_1.17.17 GenomeInfoDb_1.1.6 IRanges_1.99.15 [4] S4Vectors_0.0.8 BiocGenerics_0.11.2 loaded via a namespace (and not attached): [1] stats4_3.1.0 XVector_0.5.6
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