can not coerce CompressedIntegerList to vector or integer in 'IRanges' package
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li lilingdu ▴ 450
@li-lilingdu-1884
Last seen 6.6 years ago
can not coerce "CompressedIntegerList" to vector or integer #==================================== ranges <- IRanges(c(1,2,3),c(4,5,6)) filter <- c(1L, 0L, 1L) score <- c(10L, 2L, NA) range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5)) both <- c(ranges, range2) score <- c(score, c(0L, 3L, NA, 22L)) filter <- c(filter, c(0L, 1L, NA, 0L)) chrom <- paste("chr", rep(c(1,2), c(length(ranges), length(range2))), sep="") rd <- RangedData(both, score, filter, space = chrom, universe = "hg18") start(ranges(rd))->inter as.vector(inter) #Error in as.vector(inter) : # no method for coercing this S4 class to a vector as.integer(inter) #Error in as.integer(inter) : # cannot coerce type 'S4' to vector of type 'integer' #==================================== sessionInfo() R version 2.10.0 Under development (unstable) (2009-09-14 r49685) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.5.14 RCurl_1.2-0 bitops_1.0-4.1 Rgraphviz_1.23.4 graph_1.23.4 IRanges_1.3.77 loaded via a namespace (and not attached): [1] Biobase_2.5.6 Biostrings_2.13.40 BSgenome_1.13.12 Rcompression_0.6- 0 tools_2.10.0 XML_2.6-0 --- LiGang
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Patrick Aboyoun ★ 1.6k
@patrick-aboyoun-6734
Last seen 10.3 years ago
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LiGang, The unlist command will get you what you are looking for. AtomicList objects should be thought of as typed lists (as.integer on a regular list containing integer elements will also throw an error). Using your example I get: <<full code="" given="" below="">> > inter CompressedIntegerList: 2 elements names(2): chr1 chr2 > unlist(inter) chr1 chr1 chr1 chr2 chr2 chr2 chr2 1 2 3 15 45 20 1 > unlist(inter, use.names=FALSE) [1] 1 2 3 15 45 20 1 > sessionInfo() R version 2.10.0 Under development (unstable) (2009-09-21 r49771) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IRanges_1.3.78 loaded via a namespace (and not attached): [1] tools_2.10.0 Patrick LiGang wrote: > can not coerce "CompressedIntegerList" to vector or integer > > > #==================================== > ranges <- IRanges(c(1,2,3),c(4,5,6)) > filter <- c(1L, 0L, 1L) > score <- c(10L, 2L, NA) > range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5)) > both <- c(ranges, range2) > score <- c(score, c(0L, 3L, NA, 22L)) > filter <- c(filter, c(0L, 1L, NA, 0L)) > chrom <- paste("chr", rep(c(1,2), c(length(ranges), length(range2))), sep="") > rd <- RangedData(both, score, filter, space = chrom, universe = "hg18") > > start(ranges(rd))->inter > as.vector(inter) > > #Error in as.vector(inter) : > # no method for coercing this S4 class to a vector > > as.integer(inter) > > #Error in as.integer(inter) : > # cannot coerce type 'S4' to vector of type 'integer' > #==================================== > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-09-14 r49685) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] rtracklayer_1.5.14 RCurl_1.2-0 bitops_1.0-4.1 > Rgraphviz_1.23.4 graph_1.23.4 IRanges_1.3.77 > > loaded via a namespace (and not attached): > [1] Biobase_2.5.6 Biostrings_2.13.40 BSgenome_1.13.12 Rcompression_0.6- > 0 tools_2.10.0 XML_2.6-0 > > > > > --- > LiGang > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On Tue, Sep 22, 2009 at 7:35 AM, Patrick Aboyoun <paboyoun@fhcrc.org> wrote: > LiGang, > The unlist command will get you what you are looking for. AtomicList > objects should be thought of as typed lists (as.integer on a regular list > containing integer elements will also throw an error). Calling as.integer() works on a list where all the elements are of length one, like with sapply(). This has always been surprising to me. Why would it work in one case, but not in general? The list structure is implicitly removed in both. The question is, if IRanges supported as.integer/vector etc on atomic Lists, would this be more or less surprising to the user? To me and apparently Li Gang as well, as.integer() sounds like "make this an atomic integer vector", and there is one obvious way to do that. Would introducing an inconsistency with the base R list be so bad in this case? Michael > Using your example I get: > > <<full code="" given="" below="">> > > inter > CompressedIntegerList: 2 elements > names(2): chr1 chr2 > > unlist(inter) > chr1 chr1 chr1 chr2 chr2 chr2 chr2 > 1 2 3 15 45 20 1 > > unlist(inter, use.names=FALSE) > [1] 1 2 3 15 45 20 1 > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-09-21 r49771) > i386-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] IRanges_1.3.78 > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > > > Patrick > > > > LiGang wrote: > >> can not coerce "CompressedIntegerList" to vector or integer >> >> >> #==================================== >> ranges <- IRanges(c(1,2,3),c(4,5,6)) >> filter <- c(1L, 0L, 1L) >> score <- c(10L, 2L, NA) >> range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5)) >> both <- c(ranges, range2) >> score <- c(score, c(0L, 3L, NA, 22L)) >> filter <- c(filter, c(0L, 1L, NA, 0L)) chrom <- paste("chr", rep(c(1,2), >> c(length(ranges), length(range2))), sep="") >> rd <- RangedData(both, score, filter, space = chrom, universe = "hg18") >> >> start(ranges(rd))->inter >> as.vector(inter) >> >> #Error in as.vector(inter) : # no method for coercing this S4 class to a >> vector >> >> as.integer(inter) >> >> #Error in as.integer(inter) : # cannot coerce type 'S4' to vector of type >> 'integer' >> #==================================== >> sessionInfo() >> R version 2.10.0 Under development (unstable) (2009-09-14 r49685) >> i386-pc-mingw32 >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United >> States.1252 >> attached base packages: >> [1] grid stats graphics grDevices utils datasets methods >> base >> other attached packages: >> [1] rtracklayer_1.5.14 RCurl_1.2-0 bitops_1.0-4.1 >> Rgraphviz_1.23.4 graph_1.23.4 IRanges_1.3.77 >> loaded via a namespace (and not attached): >> [1] Biobase_2.5.6 Biostrings_2.13.40 BSgenome_1.13.12 >> Rcompression_0.6- >> 0 tools_2.10.0 XML_2.6-0 >> >> >> >> --- >> LiGang >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Since it was easy to do and you guys find it useful, I just added as.logical, as.integer, as.numeric., as.complex, as.character, as.raw, and as.factor methods for AtomicList objects to BioC 2.5. Thus you can take any AtomicList type (e.g. CompressedIntegerList) and convert it to an atomic vector type by using the appropriate as.* function. This change will be available from bioconductor.org (via biocLite) tomorrow afternoon PDT or at hedgehog.fhcrc.org (via svn) immediately. Cheers, Patrick Michael Lawrence wrote: > > > On Tue, Sep 22, 2009 at 7:35 AM, Patrick Aboyoun <paboyoun at="" fhcrc.org=""> <mailto:paboyoun at="" fhcrc.org="">> wrote: > > LiGang, > The unlist command will get you what you are looking for. > AtomicList objects should be thought of as typed lists (as.integer > on a regular list containing integer elements will also throw an > error). > > > Calling as.integer() works on a list where all the elements are of > length one, like with sapply(). This has always been surprising to me. > Why would it work in one case, but not in general? The list structure > is implicitly removed in both. The question is, if IRanges supported > as.integer/vector etc on atomic Lists, would this be more or less > surprising to the user? To me and apparently Li Gang as well, > as.integer() sounds like "make this an atomic integer vector", and > there is one obvious way to do that. Would introducing an > inconsistency with the base R list be so bad in this case? > > Michael > > > Using your example I get: > > <<full code="" given="" below="">> > > inter > CompressedIntegerList: 2 elements > names(2): chr1 chr2 > > unlist(inter) > chr1 chr1 chr1 chr2 chr2 chr2 chr2 > 1 2 3 15 45 20 1 > > unlist(inter, use.names=FALSE) > [1] 1 2 3 15 45 20 1 > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-09-21 r49771) > i386-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > other attached packages: > [1] IRanges_1.3.78 > > > loaded via a namespace (and not attached): > [1] tools_2.10.0 > > > > Patrick > > > > LiGang wrote: > > can not coerce "CompressedIntegerList" to vector or integer > > > #==================================== > ranges <- IRanges(c(1,2,3),c(4,5,6)) > filter <- c(1L, 0L, 1L) > score <- c(10L, 2L, NA) > range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5)) > both <- c(ranges, range2) > score <- c(score, c(0L, 3L, NA, 22L)) > filter <- c(filter, c(0L, 1L, NA, 0L)) chrom <- paste("chr", > rep(c(1,2), c(length(ranges), length(range2))), sep="") > rd <- RangedData(both, score, filter, space = chrom, universe > = "hg18") > > start(ranges(rd))->inter > as.vector(inter) > > #Error in as.vector(inter) : # no method for coercing this S4 > class to a vector > > as.integer(inter) > > #Error in as.integer(inter) : # cannot coerce type 'S4' to > vector of type 'integer' > #==================================== > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-09-14 > r49685) i386-pc-mingw32 > locale: > [1] LC_COLLATE=English_United States.1252 > LC_CTYPE=English_United States.1252 > LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > LC_TIME=English_United States.1252 > attached base packages: > [1] grid stats graphics grDevices utils datasets > methods base > other attached packages: > [1] rtracklayer_1.5.14 RCurl_1.2-0 bitops_1.0-4.1 > Rgraphviz_1.23.4 graph_1.23.4 IRanges_1.3.77 > loaded via a namespace (and not attached): > [1] Biobase_2.5.6 Biostrings_2.13.40 BSgenome_1.13.12 > Rcompression_0.6- > 0 tools_2.10.0 XML_2.6-0 > > > > --- > LiGang > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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