[BioC] HiTC: problem with HTClist

[Martin Morgan]

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