User: svenbioinf

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Posts by svenbioinf

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Comment: C: Find hits of subject that start somewhere in the query by using GRanges / IRange
... Hi Michael! Oh, I understand what you are doing here! However: findOverlaps(start(query), subject) Here, subject has to be a IRanges object that doesnt account for strand information.  So by ranges(sub) I get the IRanges and now I have to take care of the strand information myself.   This is a ...
written 3.3 years ago by svenbioinf0
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Find hits of subject that start somewhere in the query by using GRanges / IRanges and findOverlap()
... Using findOverlaps() on a GRanges object I would like to retrive the following hits:   Sub:  -------|||||||||||||------------------ Query Ranges: Hit5: ---------||||||||||||||||||------------ Hit6: -----------|||||||||||||||||||--------- Hit4: ---------|||||||--------------------- . . . Th ...
iranges granges R findoverlaps written 3.3 years ago by svenbioinf0 • updated 3.3 years ago by Michael Lawrence11k
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Comment: C: Keep original range by using flank() on a GRanges object.
... Thank you so much Valerie, that is quite smart (-: ...
written 3.3 years ago by svenbioinf0
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Keep original range by using flank() on a GRanges object.
... Is there an easy way to obtain the flank range and the flanked range in one GRanges object after calling flank()? See the following example: > gr1 <- GRanges(c(1,1),strand=Rle(c("+","-"),c(1,1)), IRanges(c(30,120), c(70,170)),mcols=data.frame(id=c("T1","T3"))) > gr1 GRanges object with 2 ...
granges flank written 3.3 years ago by svenbioinf0 • updated 3.3 years ago by Valerie Obenchain6.7k
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Comment: C: GRanges get hits from (only) antisense strand with findOverlaps().
... This is so good! Nice and simple. Thanks a lot, Li Lilingdu! ...
written 3.3 years ago by svenbioinf0
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GRanges get hits from (only) antisense strand with findOverlaps().
... Hello guys, Given a GRanges object with 3 ranges on the "+" strand and 2 on the "-" strand: gr1 <- GRanges(c(1,1,1,1,1),strand=Rle(c("+","+","+","-","-"),c(1,1,1,1,1)), IRanges(c(1,2,10,1,1), c(8,7,15,5,5)),mcols=data.frame(id=c("T1","T3","T5","T6","T7"))) > gr1 GRanges object with 5 range ...
granges antisense findoverlaps written 3.3 years ago by svenbioinf0 • updated 3.3 years ago by li lilingdu450

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