Question: GenomicRanges request - enable ignore.strand for findOverlaps comparing query with itself?
0
gravatar for Janet Young
5.4 years ago by
Janet Young740
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Janet Young740 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
• 1.7k views
ADD COMMENTlink written 5.4 years ago by Janet Young740
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 374 users visited in the last hour