I assumed that RangedDataList was the same as "list of RangedData".
at the moment I can't coerce one into the other: as(LargeListOfSmallRangedData,'RangedDataList') Error in as(LargeListOfSmallRangedData, "RangedDataList") : no method or default for coercing "list" to "RangedDataList" so, I will have to stick to do.call(). Thank you, Ivan On Thu, Jan 6, 2011 at 10:08 AM, Michael Lawrence <[email protected]> wrote: > > > On Thu, Jan 6, 2011 at 6:46 AM, Ivan Gregoretti <[email protected]> wrote: >> >> Hi Michael, >> >> Sorry I couldn't provide more details yesterday. When I saw your post >> I was logged out from the server and already on my way out of the >> office. >> >> This is my experience with stack(). Please see below. >> >> Thank you, >> >> Ivan >> >> >> ### load relevant libraries >> library(Biostrings) >> library(BSgenome.Mmusculus.UCSC.mm9) >> >> ### define a subset of chromosomes >> someChromosomes <- c('chr1', 'chr2', 'chr3', 'chr4', 'chr5', >> 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', >> 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', >> 'chr16', 'chr17', 'chr18', 'chr19', >> 'chrX') >> >> ### generate a series of ranges at the end of the chromosomes >> LargeListOfSmallRangedData <- lapply(someChromosomes, >> >> >> function(x){RangedData(ranges=IRanges(start=seq(length(Mmusculus[[x]])-500+1, >> >> length(Mmusculus[[x]]), >> >> 100), >> >> width=100), >> space=x, >> >> distance=seq(500-100,0,-100))}) >> >> ### Peak at the first 2 elements of the list above >> LargeListOfSmallRangedData[c(1,2)] >> > > This needs to be a RangedDataList not a list of RangedData. And better use > the latest IRanges devel, otherwise I think it's broken. > >> >> ### Try to consolidate using stack(). Here is the error message >> bigRangedData <- stack(LargeListOfSmallRangedData, indName='space') >> >> Error in rep.int(names(x), lapply(x, length)) : >> unimplemented type 'NULL' in 'rep2' >> >> ### machine and OS information >> sessionInfo() >> >> R version 2.13.0 Under development (unstable) (2010-12-02 r53747) >> 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=C 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] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BSgenome.Mmusculus.UCSC.mm9_1.3.17 BSgenome_1.19.2 >> [3] GenomicRanges_1.3.7 Biostrings_2.19.2 >> [5] IRanges_1.9.17 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.11.7 >> >> >> >> >> >> >> >> On Wed, Jan 5, 2011 at 5:11 PM, Michael Lawrence >> <[email protected]> wrote: >> > That's the correct basic usage, but how about an error message or a >> > little >> > more context? >> > >> > On Wed, Jan 5, 2011 at 2:08 PM, Ivan Gregoretti <[email protected]> >> > wrote: >> >> >> >> I tried to use it to the best of my understanding: >> >> >> >> stack(LargeListOfSmallRangedData, indName='space') >> >> >> >> I think that the failure is due to misuse from my part rather than a >> >> bug. >> >> >> >> Ivan >> >> >> >> >> >> >> >> >> >> On Wed, Jan 5, 2011 at 4:51 PM, Michael Lawrence >> >> <[email protected]> wrote: >> >> > Well it would be good to see what you tried. I think there are some >> >> > critical >> >> > bug fixes to stack in devel, but not release, so I would try with >> >> > devel. >> >> > >> >> > Michael >> >> > >> >> > On Wed, Jan 5, 2011 at 1:13 PM, Ivan Gregoretti <[email protected]> >> >> > wrote: >> >> >> >> >> >> Hi Michael, >> >> >> >> >> >> Actually, I tried consolidating the list with stack() but I failed. >> >> >> Perhaps there is no need to change anything but only show how the >> >> >> consolidation is done with stack(). >> >> >> >> >> >> Would you mind showing it for the record? >> >> >> >> >> >> Thank you, >> >> >> >> >> >> Ivan >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Wed, Jan 5, 2011 at 4:05 PM, Michael Lawrence >> >> >> <[email protected]> wrote: >> >> >> > >> >> >> > >> >> >> > On Wed, Jan 5, 2011 at 12:45 PM, Ivan Gregoretti >> >> >> > <[email protected]> >> >> >> > wrote: >> >> >> >> >> >> >> >> It works. Thanks, Martin. >> >> >> >> >> >> >> >> It would be nice to have a pointer to this functionality in the >> >> >> >> documentation. For instance, when I do ?RangedData, I can see a >> >> >> >> RangedData constructor and coercion options. However, >> >> >> >> ?RangedDataList >> >> >> >> reports its constructor but no coercion. >> >> >> >> >> >> >> > >> >> >> > It's not a coercion in the strict sense. The rbind method is >> >> >> > documented >> >> >> > for >> >> >> > RangedData. Also, RangedDataList has a stack method for rbind'ing >> >> >> > them >> >> >> > and >> >> >> > adding a factor column indicating the source of each record. The >> >> >> > "unlist" >> >> >> > method on RangedDataList is a bit strange: it does a do.call(c, >> >> >> > list) >> >> >> > instead of do.call(rbind, list). I'm thinking about changing that. >> >> >> > >> >> >> > Michael >> >> >> > >> >> >> >> >> >> >> >> Again, thank you. >> >> >> >> >> >> >> >> Ivan >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Wed, Jan 5, 2011 at 3:23 PM, Martin Morgan >> >> >> >> <[email protected]> >> >> >> >> wrote: >> >> >> >> > On 01/05/2011 12:12 PM, Ivan Gregoretti wrote: >> >> >> >> >> Hello BioC listers, >> >> >> >> >> >> >> >> >> >> Is there a function that will take a list of RangedData >> >> >> >> >> instances >> >> >> >> >> and >> >> >> >> >> consolidate them into a large RangedData instance? >> >> >> >> > >> >> >> >> > do.call(rbind, LargeListOfSmallRangedData) >> >> >> >> > >> >> >> >> > ? >> >> >> >> > Martin >> >> >> >> >> >> >> >> >> >> I'm looking for this: >> >> >> >> >> >> >> >> >> >> bigRangedData <- someFunction( LargeListOfSmallRangedData ) >> >> >> >> >> >> >> >> >> >> Thank you, >> >> >> >> >> >> >> >> >> >> Ivan >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> >> Bioc-sig-sequencing mailing list >> >> >> >> >> [email protected] >> >> >> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >> >> >> > >> >> >> >> > >> >> >> >> > -- >> >> >> >> > Computational Biology >> >> >> >> > Fred Hutchinson Cancer Research Center >> >> >> >> > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> >> >> > >> >> >> >> > Location: M1-B861 >> >> >> >> > Telephone: 206 667-2793 >> >> >> >> > >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> Bioc-sig-sequencing mailing list >> >> >> >> [email protected] >> >> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >> >> > >> >> >> > >> >> > >> >> > >> > >> > > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
