Hi, The reduce function is very useful for joining neighboring ranges. However, the score information is lost after applying reduce. Is it possible to retain the score information after applying reduce? Here is an example. library(GenomicRanges) rd <- RangedData( RangesList( chrA=IRanges(start=c(1, 4, 6), width=c(3, 2, 4)), chrB=IRanges(start=c(1, 3, 6), width=c(3, 3, 4))), score=c(2, 7, 3, 1, 1, 1)) rd RangedData with 6 rows and 1 value column across 2 spaces space ranges | score <factor> <iranges> | <numeric> 1 chrA [1, 3] | 2 2 chrA [4, 5] | 7 3 chrA [6, 9] | 3 4 chrB [1, 3] | 1 5 chrB [3, 5] | 1 6 chrB [6, 9] | 1 reduce(rd, min.gap=1) RangedData with 2 rows and 0 value columns across 2 spaces space ranges | <factor> <iranges> | 1 chrA [1, 9] | 2 chrB [1, 9] | Please note that score column is missing after applying reduce. The following is with score information. space ranges | score <factor> <iranges> | <numeric> 1 chrA [1, 9] | 12 2 chrB [1, 9] | 3 Many thanks! Best regards, Julie [[alternative HTML version deleted]]

Hi, On Wed, Aug 7, 2013 at 11:29 AM, Zhu, Lihua (Julie) <julie.zhu at="" umassmed.edu=""> wrote: > Hi, > > The reduce function is very useful for joining neighboring ranges. However, the score information is lost after applying reduce. Is it possible to retain the score information after applying reduce? > > Here is an example. > > library(GenomicRanges) > > rd <- RangedData( > RangesList( > chrA=IRanges(start=c(1, 4, 6), width=c(3, 2, 4)), > chrB=IRanges(start=c(1, 3, 6), width=c(3, 3, 4))), > score=c(2, 7, 3, 1, 1, 1)) > rd > RangedData with 6 rows and 1 value column across 2 spaces > space ranges | score > <factor> <iranges> | <numeric> > 1 chrA [1, 3] | 2 > 2 chrA [4, 5] | 7 > 3 chrA [6, 9] | 3 > 4 chrB [1, 3] | 1 > 5 chrB [3, 5] | 1 > 6 chrB [6, 9] | 1 > > reduce(rd, min.gap=1) > RangedData with 2 rows and 0 value columns across 2 spaces > space ranges | > <factor> <iranges> | > 1 chrA [1, 9] | > 2 chrB [1, 9] | > > Please note that score column is missing after applying reduce. The following is with score information. > space ranges | score > <factor> <iranges> | <numeric> > 1 chrA [1, 9] | 12 > 2 chrB [1, 9] | 3 I believe similar topics like this have come up before, and the problem is that I don't think there's any general rule of thumb that can apply to merging all `mcols` from merged/reduced ranges. I guess the rule you would like to apply here is to sum the score(s) from all the combined ranges -- but why sum? One might want to average ... or take a weighted average based on length of the combined ranges, or geometric mean, or ... What would is the right thing to do here if the ranges being merged had categorical `mcols` data? -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech

As Steve said, there's no way to do this in general. However, there is a facility via the argument "with.mapping". If it is TRUE, the function will return a mapping to the original ranges, and then the merging is up to you. On Wed, Aug 7, 2013 at 11:29 AM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu>wrote: > Hi, > > The reduce function is very useful for joining neighboring ranges. > However, the score information is lost after applying reduce. Is it > possible to retain the score information after applying reduce? > > Here is an example. > > library(GenomicRanges) > > rd <- RangedData( > RangesList( > chrA=IRanges(start=c(1, 4, 6), width=c(3, 2, 4)), > chrB=IRanges(start=c(1, 3, 6), width=c(3, 3, 4))), > score=c(2, 7, 3, 1, 1, 1)) > rd > RangedData with 6 rows and 1 value column across 2 spaces > space ranges | score > <factor> <iranges> | <numeric> > 1 chrA [1, 3] | 2 > 2 chrA [4, 5] | 7 > 3 chrA [6, 9] | 3 > 4 chrB [1, 3] | 1 > 5 chrB [3, 5] | 1 > 6 chrB [6, 9] | 1 > > reduce(rd, min.gap=1) > RangedData with 2 rows and 0 value columns across 2 spaces > space ranges | > <factor> <iranges> | > 1 chrA [1, 9] | > 2 chrB [1, 9] | > > Please note that score column is missing after applying reduce. The > following is with score information. > space ranges | score > <factor> <iranges> | <numeric> > 1 chrA [1, 9] | 12 > 2 chrB [1, 9] | 3 > > Many thanks! > > Best regards, > > Julie > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]