DMRcate error: object 'annotated' not found
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Entering edit mode
Eric Smith • 0
@eric-smith-9401
Last seen 5.3 years ago
Adelaide, Australia

Hi, Can anyone help me resolve the following, thanks. I'm following The DMRcate Package User's Guide and get the following error -

library(DMRcate)
> data(dmrcatedata)
> myMs<-logit2(myBetas)
> nrow(illuminaSNPs)
[1] 153113
> nrow(myMs)
[1] 10042
> myMs.noSNPs<-rmSNPandCH(myMs,dist=2,mafcut=0.05)
> nrow(myMs.noSNPs)
[1] 9403
> patient<-factor(sub("-.*","",colnames(myMs)))
> type<-factor(sub(".*-","",colnames(myMs)))
> design<-model.matrix(~patient+type)
> myannotation<-cpg.annotate(myMs.noSNPs,analysis.type="differential",design=design,coeff=39)
Error: datatype must be one of 'array' or 'sequencing'
Error in cpg.annotate(myMs.noSNPs, analysis.type = "differential", design = design,  : 
  object 'annotated' not found
In addition: Warning messages:
1: In if (datatype == "array") { :
  the condition has length > 1 and only the first element will be used
2: In if (datatype == "sequencing") { :
  the condition has length > 1 and only the first element will be used

sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DMRcate_1.6.1              DMRcatedata_1.6.1          DSS_2.10.0                 bsseq_1.6.0                minfi_1.16.0               bumphunter_1.10.0          locfit_1.5-9.1            
 [8] iterators_1.0.8            foreach_1.4.3              Biostrings_2.38.2          XVector_0.10.0             SummarizedExperiment_1.0.1 GenomicRanges_1.22.2       GenomeInfoDb_1.6.1        
[15] IRanges_2.4.6              S4Vectors_0.8.5            lattice_0.20-33            Biobase_2.30.0             BiocGenerics_0.16.1        BiocInstaller_1.20.1      
loaded via a namespace (and not attached):
 [1] nlme_3.1-122             bitops_1.0-6             matrixStats_0.50.1       RColorBrewer_1.1-2       tools_3.2.3              doRNG_1.6                nor1mix_1.2-1            rpart_4.1-10            
 [9] Hmisc_3.17-1             DBI_0.3.1                Gviz_1.14.0              colorspace_1.2-6         nnet_7.3-11              gridExtra_2.0.0          base64_1.1               preprocessCore_1.32.0   
[17] chron_2.3-47             pkgmaker_0.22            rtracklayer_1.30.1       scales_0.3.0             genefilter_1.52.0        quadprog_1.5-5           stringr_1.0.0            digest_0.6.8            
[25] Rsamtools_1.22.0         foreign_0.8-66           illuminaio_0.12.0        siggenes_1.44.0          R.utils_2.2.0            GEOquery_2.36.0          dichromat_2.0-0          BSgenome_1.38.0         
[33] limma_3.26.3             RSQLite_1.0.0            mclust_5.1               BiocParallel_1.4.3       gtools_3.5.0             acepack_1.3-3.3          R.oo_1.19.0              VariantAnnotation_1.16.4
[41] RCurl_1.95-4.7           magrittr_1.5             Formula_1.2-1            futile.logger_1.4.1      Rcpp_0.12.2              munsell_0.4.2            proto_0.3-10             R.methodsS3_1.7.0       
[49] stringi_1.0-1            MASS_7.3-45              zlibbioc_1.16.0          plyr_1.8.3               grid_3.2.3               multtest_2.26.0          GenomicFeatures_1.22.7   annotate_1.48.0         
[57] beanplot_1.2             igraph_1.0.1             rngtools_1.2.4           corpcor_1.6.8            codetools_0.2-14         biomaRt_2.26.1           mixOmics_5.2.0           futile.options_1.0.0    
[65] XML_3.98-1.3             biovizBase_1.18.0        latticeExtra_0.6-26      lambda.r_1.1.7           data.table_1.9.6         gtable_0.1.2             reshape_0.8.5            ggplot2_2.0.0           
[73] xtable_1.8-0             survival_2.38-3          GenomicAlignments_1.6.1  AnnotationDbi_1.32.2     registry_0.3             ellipse_0.3-8            cluster_2.0.3            rgl_0.95.1429 
dmrcate error • 987 views
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Entering edit mode
Tim Peters ▴ 120
@tim-peters-7579
Last seen 4 months ago
Australia

Hi Eric,

I've recently updated the DMRcate package and so some cosmetic changes have been added to the 450K workflow to distinguish it from the sequencing workflow. Please use the new vignette here. http://bioconductor.org/packages/3.2/bioc/vignettes/DMRcate/inst/doc/DMRcate.pdf

 

Best,

Tim

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Entering edit mode

Excellent, thanks Tim.

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