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
>
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