HiTC: problem with HTClist
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@hermann-norpois-5726
Last seen 7.1 years ago
Germany
Hello, I was interested in reading some 5C matrix-files and I did not even manage the example of the tutorial because the "function HTClist" was not found (see http://www.bioconductor.org/packages/devel/bioc/vignettes/HiTC/inst/do c/HiTC.pdf ). What's wrong with ... > l <- sapply (list.files (exDir, pattern=paste ("HIC_gm06690_"), full.names=TRUE), import.my5C) Convert my5C matrix file in HiTC object(s) Loading chr14-chr14... > hiC <- HTClist(l) Fehler: konnte Funktion "HTClist" nicht finden # function "HTClist" not found. > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] HiTC_1.2.0 girafe_1.10.0 genomeIntervals_1.14.0 [4] intervals_0.13.3 ShortRead_1.16.3 latticeExtra_0.6-24 [7] RColorBrewer_1.0-5 lattice_0.20-13 Rsamtools_1.10.2 [10] Biostrings_2.26.3 GenomicRanges_1.10.6 IRanges_1.16.4 [13] BiocGenerics_0.4.0 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] Biobase_2.18.0 bitops_1.0-5 BSgenome_1.26.1 colorspace_1.2-1 [5] compiler_2.15.2 dichromat_2.0-0 digest_0.6.2 ggplot2_0.9.3 [9] gtable_0.1.2 hwriter_1.3 labeling_0.1 MASS_7.3-23 [13] memoise_0.1 munsell_0.4 parallel_2.15.2 plyr_1.8 [17] proto_0.3-10 reshape2_1.2.2 scales_0.2.3 stats4_2.15.2 [21] stringr_0.6.2 tools_2.15.2 zlibbioc_1.4.0 Actually I would just like to open a 5C-matrix file (and maybe the primer files as well). No Bamfile. Can you help me? Thanks Hermann [[alternative HTML version deleted]]
HiTC HiTC • 921 views
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@martin-morgan-1513
Last seen 4 days ago
United States
Hi Hermann -- On 02/04/2013 09:17 AM, Hermann Norpois wrote: > Hello, > > I was interested in reading some 5C matrix-files and I did not even manage > the example of the tutorial because the "function HTClist" was not found > (see > http://www.bioconductor.org/packages/devel/bioc/vignettes/HiTC/inst/ doc/HiTC.pdf the vignette is from the 'devel' repository, but... > ). > > What's wrong with ... > > >> l <- sapply (list.files (exDir, pattern=paste ("HIC_gm06690_"), > full.names=TRUE), import.my5C) > Convert my5C matrix file in HiTC object(s) > Loading chr14-chr14... >> hiC <- HTClist(l) > Fehler: konnte Funktion "HTClist" nicht finden # function "HTClist" not > found. >> sessionInfo() > R version 2.15.2 (2012-10-26) ...you're using the 'release' version of R and hence Bioc. So either update R and Bioconductor, or follow the vignette corresponding to your version of the package, e.g., vignette(package="HiTC") # one vignette, "HiTC" vignette(package="HiTC", "HiTC") > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] HiTC_1.2.0 girafe_1.10.0 genomeIntervals_1.14.0 > [4] intervals_0.13.3 ShortRead_1.16.3 latticeExtra_0.6-24 > [7] RColorBrewer_1.0-5 lattice_0.20-13 Rsamtools_1.10.2 > [10] Biostrings_2.26.3 GenomicRanges_1.10.6 IRanges_1.16.4 > [13] BiocGenerics_0.4.0 BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] Biobase_2.18.0 bitops_1.0-5 BSgenome_1.26.1 colorspace_1.2-1 > [5] compiler_2.15.2 dichromat_2.0-0 digest_0.6.2 ggplot2_0.9.3 > [9] gtable_0.1.2 hwriter_1.3 labeling_0.1 MASS_7.3-23 > [13] memoise_0.1 munsell_0.4 parallel_2.15.2 plyr_1.8 > [17] proto_0.3-10 reshape2_1.2.2 scales_0.2.3 stats4_2.15.2 > [21] stringr_0.6.2 tools_2.15.2 zlibbioc_1.4.0 > > > Actually I would just like to open a 5C-matrix file (and maybe the primer > files as well). No Bamfile. Can you help me? > > Thanks Hermann > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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