[BioC] methyAnalysis - changes to GenoSet

[Martin Morgan]

On 03/07/2013 08:23 PM, Lavinia Gordon wrote:
> 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

typo -- methyGenoSet.sm

Martin

>> 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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