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
).

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

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