Question

DNAStringSetList can't coerce a list?

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Taylor, Sean D ▴ 250

@taylor-sean-d-5800

Last seen 10.2 years ago

Hi Herve, It seems like I used to be able to coerce a list of DNA String Sets into a DNAStringSetList. With the latest build though it seems like that is no longer the case: > dna1 <- c("AAA", "AC", "", "T", "GGATA") > dna2 <- c("G", "TT", "C") > foo<-DNAStringSet(dna1) > bar<-DNAStringSet(dna2) > DNAStringSetList(foo, bar) DNAStringSetList of length 2 [[1]] AAA AC T GGATA [[2]] G TT C > baz<-list(foo, bar) > DNAStringSetList(baz) Error in IRanges:::new_XVectorList_from_list_of_XVector(tmp_class, x) : all elements in 'x' must be DNAString objects Thanks, Sean Sean Taylor Post-doctoral Fellow Fred Hutchinson Cancer Research Center 206-667-5544 [[alternative HTML version deleted]]

Cancer Cancer • 1.1k views

ADD COMMENT • link 11.3 years ago Taylor, Sean D ▴ 250

score 0 · Answer 1 · 2013-08-05

Sorry, here is my sessionInfo() > sessionInfo() R version 3.0.1 (2013-05-16) 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] XVector_0.1.0 BiocInstaller_1.11.4 ShortRead_1.19.10 [4] latticeExtra_0.6-24 RColorBrewer_1.0-5 lattice_0.20-15 [7] Rsamtools_1.13.27 Biostrings_2.29.14 GenomicRanges_1.13.35 [10] IRanges_1.19.20 BiocGenerics_0.7.3 magicaxis_1.5 loaded via a namespace (and not attached): [1] Biobase_2.20.0 bitops_1.0-5 grid_3.0.1 hwriter_1.3 stats4_3.0.1 [6] tools_3.0.1 zlibbioc_1.6.0 From: Taylor, Sean D Sent: Monday, August 05, 2013 4:58 PM To: bioconductor@r-project.org Cc: Pages, Herve (hpages@fhcrc.org) Subject: DNAStringSetList can't coerce a list? Hi Herve, It seems like I used to be able to coerce a list of DNA String Sets into a DNAStringSetList. With the latest build though it seems like that is no longer the case: > dna1 <- c("AAA", "AC", "", "T", "GGATA") > dna2 <- c("G", "TT", "C") > foo<-DNAStringSet(dna1) > bar<-DNAStringSet(dna2) > DNAStringSetList(foo, bar) DNAStringSetList of length 2 [[1]] AAA AC T GGATA [[2]] G TT C > baz<-list(foo, bar) > DNAStringSetList(baz) Error in IRanges:::new_XVectorList_from_list_of_XVector(tmp_class, x) : all elements in 'x' must be DNAString objects Thanks, Sean Sean Taylor Post-doctoral Fellow Fred Hutchinson Cancer Research Center 206-667-5544 [[alternative HTML version deleted]]

score 0 · Answer 2 · 2013-08-06

Nevermind. I restarted my R session and that seems to have helped. From: Taylor, Sean D Sent: Monday, August 05, 2013 4:59 PM To: bioconductor@r-project.org Cc: Pages, Herve (hpages@fhcrc.org) Subject: RE: DNAStringSetList can't coerce a list? Sorry, here is my sessionInfo() > sessionInfo() R version 3.0.1 (2013-05-16) 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] XVector_0.1.0 BiocInstaller_1.11.4 ShortRead_1.19.10 [4] latticeExtra_0.6-24 RColorBrewer_1.0-5 lattice_0.20-15 [7] Rsamtools_1.13.27 Biostrings_2.29.14 GenomicRanges_1.13.35 [10] IRanges_1.19.20 BiocGenerics_0.7.3 magicaxis_1.5 loaded via a namespace (and not attached): [1] Biobase_2.20.0 bitops_1.0-5 grid_3.0.1 hwriter_1.3 stats4_3.0.1 [6] tools_3.0.1 zlibbioc_1.6.0 From: Taylor, Sean D Sent: Monday, August 05, 2013 4:58 PM To: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Cc: Pages, Herve (hpages@fhcrc.org<mailto:hpages@fhcrc.org>) Subject: DNAStringSetList can't coerce a list? Hi Herve, It seems like I used to be able to coerce a list of DNA String Sets into a DNAStringSetList. With the latest build though it seems like that is no longer the case: > dna1 <- c("AAA", "AC", "", "T", "GGATA") > dna2 <- c("G", "TT", "C") > foo<-DNAStringSet(dna1) > bar<-DNAStringSet(dna2) > DNAStringSetList(foo, bar) DNAStringSetList of length 2 [[1]] AAA AC T GGATA [[2]] G TT C > baz<-list(foo, bar) > DNAStringSetList(baz) Error in IRanges:::new_XVectorList_from_list_of_XVector(tmp_class, x) : all elements in 'x' must be DNAString objects Thanks, Sean Sean Taylor Post-doctoral Fellow Fred Hutchinson Cancer Research Center 206-667-5544 [[alternative HTML version deleted]]