methyAnalysis

headers Lavinia Gordon | 8 Mar 2013 05:23

Dear Bioc users,
I have just tried the example code supplied with the package methyAnalysis and am getting an error:

> ###################################################
> ### code chunk number 3: Slide-window smoothing of the DNA methylation data
> ###################################################
> methyGenoSet.sm <- smoothMethyData(exampleMethyGenoSet, winSize = 250)
Smoothing Chromosome 21 ...

Note: Method with signature âGenoSet#character#ANY#ANYâ chosen for function â[â,
target signature âMethyGenoSet#character#character#missingâ.
"MethyGenoSet#ANY#ANY#ANY" would also be valid
Warning message:
The ranges method on a GenoSet is depricated. Please use space(locData(x)) or seqnames(locData(x)) as
appropriate for RangedData or GRanges.
> methyGenoset.sm
Error: object 'methyGenoset.sm' not found
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8
 [2] LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8
 [6] LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C
 [8] LC_NAME=C
 [9] LC_ADDRESS=C
[10] LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8
[12] LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats     graphics  grDevices
[5] utils     datasets  methods   base

other attached packages:
[1] methyAnalysis_1.0.0  org.Hs.eg.db_2.8.0
[3] RSQLite_0.11.2       DBI_0.2-5
[5] AnnotationDbi_1.20.5 Biobase_2.18.0
[7] IRanges_1.16.6       BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] affy_1.36.1            affyio_1.26.0
 [3] annotate_1.36.0        BiocInstaller_1.8.3
 [5] biomaRt_2.14.0         Biostrings_2.26.3
 [7] biovizBase_1.6.2       bitops_1.0-5
 [9] BSgenome_1.26.1        cluster_1.14.3
[11] colorspace_1.2-1       dichromat_2.0-0
[13] genefilter_1.40.0      GenomicFeatures_1.10.2
[15] GenomicRanges_1.10.7   genoset_1.10.1
[17] Gviz_1.2.1             Hmisc_3.10-1
[19] KernSmooth_2.23-9      labeling_0.1
[21] lattice_0.20-13        lumi_2.10.0
[23] MASS_7.3-23            Matrix_1.0-11
[25] methylumi_2.4.0        mgcv_1.7-22
[27] munsell_0.4            nleqslv_2.0
[29] nlme_3.1-108           parallel_2.15.2
[31] plyr_1.8               preprocessCore_1.20.0
[33] RColorBrewer_1.0-5     RCurl_1.95-4.1
[35] Rsamtools_1.10.2       rtracklayer_1.18.2
[37] scales_0.2.3           splines_2.15.2
[39] stats4_2.15.2          stringr_0.6.2
[41] survival_2.37-4        tools_2.15.2
[43] XML_3.95-0.2           xtable_1.7-1
[45] zlibbioc_1.4.0
>

With regards,

Lavinia Gordon
Senior Research Officer
Quantitative Sciences Core, Bioinformatics

Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road Parkville Victoria 3052 Australia
T 03 8341 6221
www.mcri.edu.au<http://www.mcri.edu.au/>

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methyAnalysis - changes to GenoSet