User: lovro0

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lovro010
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New User
Location:
Slovenia/Ljubljana/Clinical institute of medical genetics
Last seen:
4 months, 2 weeks ago
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1 year ago
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l*****@gmail.com

Posts by lovro0

<prev • 14 results • page 1 of 2 • next >
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Comment: C: behaviour of findOverlaps on GRangesList object
... Thank you for all your prompt replies! Unfortunately i got hit by the following: "Sorry! Your posting limit of (5) posts per six hours has been reached." Anyhow: I have around 1500 probands and a result for each of them is generated by an external algorithm. These results are then parsed into tab ...
written 5 months ago by lovro010
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Comment: C: behaviour of findOverlaps on GRangesList object
... Oh. Thank you! I wasn't aware that any "within the list element" overlapping check is done. Is there any way I can avoid this? I am curious how is this useful? A random input is ignored despite having an overlap with a feature just because it also has an overlap with another input that happens to b ...
written 5 months ago by lovro010
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Comment: C: behaviour of findOverlaps on GRangesList object
... I have tried this and every element of the list produces a hit: Over12 <- findOverlaps(RGRreal,Mranges, select = "first") > length(Over12) [1] 1441 This was expected since every element in RGRreal contains at least one range and all of them were used to create Mranges. Furthermore, unliste ...
written 5 months ago by lovro010
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Comment: C: behaviour of findOverlaps on GRangesList object
... This is the "Over" object: > Over Hits object with 10522 hits and 0 metadata columns:           queryHits subjectHits           <integer>   <integer>       [1]         1          17       [2]         1          42       [3]         1         687       [4]         1         879       ...
written 5 months ago by lovro010
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Comment: C: behaviour of findOverlaps on GRangesList object
... I'm sorry, I forgot to mention this. The Mranges object was made as an union of all intervals in RGRreal object. It was produced with "bedtools merge". Therefore each input range should intersect at least the the Mranges interval it contributed to in bedtools merge. I did this because i wanted to c ...
written 5 months ago by lovro010
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behaviour of findOverlaps on GRangesList object
... hi, problem: findOverlaps() used on GRangesList and GRanges object returns a hits object which is too short (10522 instead of 10596 )     > class(RGRreal)     [1] "GRangesList"     attr(,"package")     [1] "GenomicRanges"     > class(Mranges)     [1] "GRanges"     attr(,"package")     [1] "G ...
genomicranges grangeslist findoverlaps written 5 months ago by lovro010
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Comment: C: How do I merge a list of GRanges?
... do.call method did not work for me (the result remained a list), however, the following from "GRangesList-class {GenomicRanges}"  R documentation did: "unlist(x, recursive = TRUE, use.names = TRUE): Concatenates the elements of x into a single GRanges object." I'm still looking for a method to pro ...
written 5 months ago by lovro010
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Comment: C: how to make findOverlaps from genomicAlignments package to consider soft-clipped
... Yes, I'm trying to select read pairs which span the breakpoint of an insertion (which is not in the reference genome) for further analysis. I want to differentiate between reads which overhang into the putative insertion by at least, say, 35bp and those that don't. Some of the insertions I'm genotyp ...
written 11 months ago by lovro010
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Comment: C: how to make findOverlaps from genomicAlignments package to consider soft-clipped
... Hi, I appreciate your help, however I haven't been able to solve the problem yet. maxgap wouldn't do anything for me, since I need to differentiate between reads which extend over the breakpoint with at least 35bp overhang, and those that extend over less. All reads that extend over the breakpoint ...
written 11 months ago by lovro010
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Comment: C: how to make findOverlaps from genomicAlignments package to consider soft-clipped
... > TEST<-granges(BAMs[[1]]) Error in .local(x, use.names, use.mcols, ...) :   For some pairs in 'x', the 2 alignments are not on the same chromosome. Cannot   associate a unique genomic range to such pairs. Please call granges() with   'on.discordant.seqnames="drop"' to drop these pairs, or wit ...
written 11 months ago by lovro010

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