Hi Juan

You need to try the latest developing version of methyAnalysis package. For
some unknown reason, the Bioc reports some checking error of the vignette.
So the latest developing version is not available through biocLite. It will
send the package to you in another email. Thanks for reporting the problem!

Pan


On Tue, Nov 12, 2013 at 1:11 PM, jfertaj <jfernandezt@udc.es> wrote:

> Dear list and Pan,
>
> I’m still having some problems with the methyAnalysis package, after
> update some functions thanks to Pan I’m still experiencing some problems
> with certain functions, for example I am not able to plot the heatmap with
>
> >heatmapByChromosome(methyGenoSet, gene='55342',
> genomicFeature='TxDb.Hsapiens.UCSC.hg19.knownGene', includeGeneBody=TRUE)
> Error in .local(range, ...) : could not find function "restoreSeqlevels"
> Error: could not find function "restoreSeqlevels"
>
> or annotate the DMR regions with
>
>  >DMRInfo.ann <- annotateDMRInfo(allDMRInfo,
> 'TxDb.Hsapiens.UCSC.hg19.knownGene')
> There were 50 or more warnings (use warnings() to see the first 50)
> Error in IRanges::as.matrix(nearest(grange[naInd], tr, select = "all")) :
>   error in evaluating the argument 'x' in selecting a method for function
> 'as.matrix': Error in mergeNamedAtomicVectors(genome(x), genome(y), what =
> c("sequence",  :
>   sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10,
> chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20,
> chr21, chr22, chrX, chrY have incompatible genomes:
>   - in 'x': , , , , , , , , , , , , , , , , , , , , , , ,
>   - in 'y': hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19,
> hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19,
> hg19, hg19
>
> Here is my sessionInfo()
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] parallel  grid      stats     graphics  grDevices utils     datasets
>  methods   base
>
> other attached packages:
>  [1] IlluminaHumanMethylation450k.db_2.0.7
> FDb.InfiniumMethylation.hg19_2.0.10   BSgenome.Hsapiens.UCSC.hg19_1.3.19
>  BSgenome_1.28.0
>  [5] Biostrings_2.28.0                     GenomicFeatures_1.12.3
>        plyr_1.8                              pheatmap_0.7.7
>
>  [9] genefilter_1.42.0                     multtest_2.18.0
>       annotate_1.38.0                       GOstats_2.26.0
>
> [13] graph_1.38.3                          Category_2.26.0
>       IlluminaHumanMethylation27k.db_1.4.7  limma_3.16.6
>
> [17] lumi_2.14.0                           methylumi_2.8.0
>       matrixStats_0.8.5                     ggplot2_0.9.3.1
>
> [21] reshape2_1.2.2                        scales_0.2.3
>        methyAnalysis_1.4.0                   org.Hs.eg.db_2.9.0
>
> [25] RSQLite_0.11.4                        DBI_0.2-7
>       AnnotationDbi_1.22.6                  Biobase_2.20.1
>
> [29] GenomicRanges_1.12.4                  IRanges_1.20.2
>        BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
>  [1] affy_1.38.1           affyio_1.28.0         AnnotationForge_1.2.2
> base64_1.1            beanplot_1.1          BiocInstaller_1.10.3
>  biomaRt_2.16.0
>  [8] biovizBase_1.8.1      bitops_1.0-6          bumphunter_1.2.0
>  cluster_1.14.4        codetools_0.2-8       colorspace_1.2-2
>  dichromat_2.0-0
> [15] digest_0.6.3          doRNG_1.5.5           foreach_1.4.1
> genoset_1.14.0        GO.db_2.9.0           GSEABase_1.22.0
> gtable_0.1.2
> [22] Gviz_1.6.0            Hmisc_3.12-2          illuminaio_0.4.0
>  iterators_1.0.6       itertools_0.1-1       KernSmooth_2.23-10
>  labeling_0.2
> [29] lattice_0.20-23       latticeExtra_0.6-26   locfit_1.5-9.1
>  MASS_7.3-29           Matrix_1.0-14         mclust_4.2
>  mgcv_1.7-26
> [36] minfi_1.8.3           munsell_0.4.2         nleqslv_2.0
> nlme_3.1-111          nor1mix_1.1-4         pkgmaker_0.17.4
> preprocessCore_1.22.0
> [43] proto_0.3-10          R.methodsS3_1.4.4     RBGL_1.36.2
> RColorBrewer_1.0-5    RCurl_1.95-4.1        registry_0.2
>  reshape_0.8.4
> [50] rngtools_1.2.3        rpart_4.1-3           Rsamtools_1.12.3
>  rtracklayer_1.20.4    siggenes_1.36.0       splines_3.0.2
> stats4_3.0.2
> [57] stringr_0.6.2         survival_2.37-4       tools_3.0.2
> XML_3.95-0.2          xtable_1.7-1          XVector_0.2.0
> zlibbioc_1.6.0
>
> Thanks
>
> Juan
> ---
> Juan Fernandez Tajes, phD
> Grupo Xenomar – Área de Genética
> Facultad de Ciencias – A Zapateira
> Universidad de A Coruña
> Spain
> Tlf - +34 981 16700
> Email: Jfernandezt@udc.es
>
>

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