Hello again, Please ignore this thread. It turns out that I was using a Biostrings version where Views was in the process of being modified. I just re-installed Biostrings and Views works correctly using R 2.14.0devel.
Sorry for the spam >.< Leonardo R 2.14.0devel code with today's packages from biocLite() > library(Biostrings) Loading required package: IRanges Attaching package: IRanges The following object(s) are masked from package:base: cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union > dna <- DNAString("ATCG") > ir <- IRanges(1:2, width=2) > ir IRanges of length 2 start end width [1] 1 2 2 [2] 2 3 2 > Views(dna, ir) Views on a 4-letter DNAString subject subject: ATCG views: start end width [1] 1 2 2 [AT] [2] 2 3 2 [TC] > DNAStringSet(Views(dna, ir)) A DNAStringSet instance of length 2 width seq [1] 2 AT [2] 2 TC ### What I want to do works well now in R 2.14.0devel :D ### The examples for XStringViews have warnings but those are intended! > example(XStringViews) XStrnV> v12 <- Views(DNAString("TAATAATG"), start=-2:9, end=0:11) XStrnV> ## Do not do this anymore: XStrnV> if (interactive()) { XStrnV+ XStringViews(v12, subjectClass="RNAString") # DEPRECATED! XStrnV+ } Views on a 8-letter RNAString subject subject: UAAUAAUG views: start end width [1] -2 0 3 [ ] [2] -1 1 3 [ U] [3] 0 2 3 [ UA] [4] 1 3 3 [UAA] [5] 2 4 3 [AAU] [6] 3 5 3 [AUA] [7] 4 6 3 [UAA] [8] 5 7 3 [AAU] [9] 6 8 3 [AUG] [10] 7 9 3 [UG ] [11] 8 10 3 [G ] [12] 9 11 3 [ ] XStrnV> ## Do this instead: XStrnV> xsbasetype(v12) <- "RNA" XStrnV> ## Do not do this anymore: XStrnV> if (interactive()) { XStrnV+ XStringViews(AAString("MARKSLEMSIR*")) # DEPRECATED! XStrnV+ } Views on a 12-letter AAString subject subject: MARKSLEMSIR* views: start end width [1] 1 12 12 [MARKSLEMSIR*] XStrnV> ## Do this instead: XStrnV> as(AAString("MARKSLEMSIR*"), "Views") Views on a 12-letter AAString subject subject: MARKSLEMSIR* views: start end width [1] 1 12 12 [MARKSLEMSIR*] XStrnV> x <- c("abcdefghij", "KLMN") XStrnV> ## Do not do this anymore: XStrnV> if (interactive()) { XStrnV+ XStringViews(x, subjectClass="BString") # DEPRECATED! XStrnV+ } Views on a 14-letter BString subject subject: abcdefghijKLMN views: start end width [1] 1 10 10 [abcdefghij] [2] 11 14 4 [KLMN] XStrnV> ## Do this instead (if you really want views): XStrnV> as(BStringSet(x), "Views") Views on a 14-letter BString subject subject: abcdefghijKLMN views: start end width [1] 1 10 10 [abcdefghij] [2] 11 14 4 [KLMN] XStrnV> ## otherwise just do: XStrnV> BStringSet(x) A BStringSet instance of length 2 width seq [1] 10 abcdefghij [2] 4 KLMN Warning messages: 1: Using XStringViews(..., subjectClass="RNAString") on an XStringViews object is deprecated. Please use 'xsbasetype(x) <- "RNA"' instead. 2: Using XStringViews() on a AAString object is deprecated. Please use 'as(x, "Views")' instead. 3: Using XStringViews() on a character vector is deprecated. Please use instead something like: as(BStringSet(x)), "Views") if you really want views, otherwise just: BStringSet(x) > ?XStringViews starting httpd help server ... done > sessionInfo() R version 2.14.0 Under development (unstable) (2011-06-09 r56106) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Biostrings_2.21.6 IRanges_1.11.10 loaded via a namespace (and not attached): [1] tools_2.14.0 > On Mon, Jun 20, 2011 at 11:24 AM, Leonardo Collado Torres < lcoll...@lcg.unam.mx> wrote: > Hello Bioc-sig list, > > I am unable to use Views on a DNAString object using R 2.14.0devel I > believe that the error is unintended because it pops up when running the > XStringViews examples. The same code works well in R 2.12.0 and 2.13.0 > > If the error is not intended, then please teach me how to solve it. > > Thank you and greetings, > Leonardo > > > 2.14.0devel code: > > > > library(Biostrings) > Loading required package: IRanges > > Attaching package: IRanges > > The following object(s) are masked from package:base: > > cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, > pmin, pmin.int, rbind, rep.int, setdiff, table, union > > > dna <- DNAString("ATCG") > > ir <- IRanges(1:2, width=2) > > ir > IRanges of length 2 > start end width > [1] 1 2 2 > [2] 2 3 2 > > > > Views(dna, start = start(ir), end = end(ir)) > Error in initialize(value, ...) : > invalid names for slots of class "XStringViews": ranges > > Views(dna, ir) > Error in initialize(value, ...) : > invalid names for slots of class "XStringViews": ranges > > ### From the error message I thought that maybe it was a matter of adding > "names" After all, Views does have a "names" argument. > ### However, the error is still there. > > > args(Views) > function (subject, start = NULL, end = NULL, width = NULL, names = NULL) > NULL > > Views(dna, start = start(ir), end = end(ir), names = letters[1:2]) > Error in initialize(value, ...) : > invalid names for slots of class "XStringViews": ranges > > > > ?XStringViews > starting httpd help server ... done > > example(XStringViews) > > XStrnV> v12 <- Views(DNAString("TAATAATG"), start=-2:9, end=0:11) > Error in initialize(value, ...) : > invalid names for slots of class "XStringViews": ranges > > sessionInfo() > R version 2.14.0 Under development (unstable) (2011-06-09 r56106) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.21.4 IRanges_1.11.8 > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > > > > > > > R 2.12.0 code: > > > > > > library(Biostrings) > Loading required package: IRanges > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:base': > > cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin, > pmin.int, rbind, rep.int, table > > > dna <- DNAString("ATCG") > > ir <- IRanges(1:2, width=2) > > ir > IRanges of length 2 > start end width > [1] 1 2 2 > [2] 2 3 2 > > Views(dna, start = start(ir), end = end(ir)) > Views on a 4-letter DNAString subject > subject: ATCG > views: > start end width > [1] 1 2 2 [AT] > [2] 2 3 2 [TC] > > DNAStringSet(Views(dna, start = start(ir), end = end(ir))) > A DNAStringSet instance of length 2 > width seq > [1] 2 AT > [2] 2 TC > > Views(dna, ir) > Views on a 4-letter DNAString subject > subject: ATCG > views: > start end width > [1] 1 2 2 [AT] > [2] 2 3 2 [TC] > > example(XStringViews) > > XStrnV> v12 <- Views(DNAString("TAATAATG"), start=-2:9, end=0:11) > > XStrnV> XStringViews(v12, subjectClass="RNAString") > Views on a 8-letter RNAString subject > subject: UAAUAAUG > views: > start end width > [1] -2 0 3 [ ] > [2] -1 1 3 [ U] > [3] 0 2 3 [ UA] > [4] 1 3 3 [UAA] > [5] 2 4 3 [AAU] > [6] 3 5 3 [AUA] > [7] 4 6 3 [UAA] > [8] 5 7 3 [AAU] > [9] 6 8 3 [AUG] > [10] 7 9 3 [UG ] > [11] 8 10 3 [G ] > [12] 9 11 3 [ ] > > XStrnV> XStringViews(AAString("MARKSLEMSIR*")) > Views on a 12-letter AAString subject > subject: MARKSLEMSIR* > views: > start end width > [1] 1 12 12 [MARKSLEMSIR*] > > XStrnV> XStringViews("abcdefghij", subjectClass="BString") > Views on a 10-letter BString subject > subject: abcdefghij > views: > start end width > [1] 1 10 10 [abcdefghij] > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.18.0 IRanges_1.8.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 tools_2.12.0 > > > > > > > > > > > R 2.13.0 code > > > > library(Biostrings) > Loading required package: IRanges > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:base': > > cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, > pmin, pmin.int, rbind, rep.int, setdiff, table, union > > > dna <- DNAString("ATCG") > > ir <- IRanges(1:2, width=2) > > ir > IRanges of length 2 > start end width > [1] 1 2 2 > [2] 2 3 2 > > Views(dna, ir) > Views on a 4-letter DNAString subject > subject: ATCG > views: > start end width > [1] 1 2 2 [AT] > [2] 2 3 2 [TC] > > DNAStringSet(Views(dna, ir)) > A DNAStringSet instance of length 2 > width seq > [1] 2 AT > [2] 2 TC > > example(XStringViews) > > XStrnV> v12 <- Views(DNAString("TAATAATG"), start=-2:9, end=0:11) > > XStrnV> XStringViews(v12, subjectClass="RNAString") > Views on a 8-letter RNAString subject > subject: UAAUAAUG > views: > start end width > [1] -2 0 3 [ ] > [2] -1 1 3 [ U] > [3] 0 2 3 [ UA] > [4] 1 3 3 [UAA] > [5] 2 4 3 [AAU] > [6] 3 5 3 [AUA] > [7] 4 6 3 [UAA] > [8] 5 7 3 [AAU] > [9] 6 8 3 [AUG] > [10] 7 9 3 [UG ] > [11] 8 10 3 [G ] > [12] 9 11 3 [ ] > > XStrnV> XStringViews(AAString("MARKSLEMSIR*")) > Views on a 12-letter AAString subject > subject: MARKSLEMSIR* > views: > start end width > [1] 1 12 12 [MARKSLEMSIR*] > > XStrnV> XStringViews("abcdefghij", subjectClass="BString") > Views on a 10-letter BString subject > subject: abcdefghij > views: > start end width > [1] 1 10 10 [abcdefghij] > > sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Biostrings_2.20.1 IRanges_1.10.4 > > loaded via a namespace (and not attached): > [1] tools_2.13.0 > > > > [[alternative HTML version deleted]]
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