User: gueux

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Posts by gueux

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Comment: C: Aggregating scores of multiple metadata columns from one GRanges object on anoth
... thanks, that does work to associate the matrix but then if I have more score columns than rows in `roi` then I get the error `Error in DataFrame(by, stats) : different row counts implied by arguments`. It seems, the result is transposed with the result for interval 1 placed in column 1 vertically in ...
written 5 months ago by gueux0
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Comment: C: Aggregating scores of multiple metadata columns from one GRanges object on anoth
... Doing this still ends up with tomap having 5 metadata columns: `tomap <- GRanges( seqnames = Rle(c("chr1"), c(10)), ranges = IRanges(1:10*10, end = 1:10*10+5)) mcols(tomap)<-scores` Then running: `aggregate(tomap, hits, max_scores=lapply(scores, colMaxs))` gives this error: `Error ...
written 5 months ago by gueux0
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Comment: C: Aggregating scores of multiple metadata columns from one GRanges object on anoth
... Thanks Michael, but how do you store a matrix as a single column in the GRanges? If I do: `scores<-cbind(score1 = runif(10),score2=runif(10),score3=runif(10),score4=runif(10),score5=runif(10))` and then: `tomap <- GRanges( seqnames = Rle(c("chr1"), c(10)), ranges = IRanges(1:10*10, ...
written 5 months ago by gueux0
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Answer: A: Aggregating scores of multiple metadata columns from one GRanges object on anoth
... Based on a suggestion received [here][1], the following works: ``` scoreagg<-paste0("mcols(ans)<-aggregate(tomap,hits,",paste0(colnames(tomap@elementMetadata)[1:5],"=","max(",colnames(tomap@elementMetadata)[1:5],")",collapse=","),")") eval(parse(text=scoreagg)) ``` [1]: https://stackoverf ...
written 5 months ago by gueux0
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Aggregating scores of multiple metadata columns from one GRanges object on another
... I have one GRanges object with thousands of score columns (tomap), and another with regions of interest and no metadata (roi). I am trying to map the max score from each column in tomap to the corresponding interval in roi. I also want to retain the names of the score columns (in my real data these ...
genomicranges written 5 months ago by gueux0 • updated 5 months ago by Michael Lawrence11k

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