I have been trying to load minfi, lumi, methylumi and DMRcate packages in Rstudio. These packages are already installed and I have been using it for a while now. However, when I try to load them this past week I have been encountering errors stating - "Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘data.table".
In addition, I have also been encountering problems with DMRcate functions due to error in loading the annotation packages - IlluminaHumanMethylationEPICanno.ilm10b2.hg19 and IlluminaHumanMethylation450kanno.ilmn12.hg19.
I have tried uninstalling and reinstalling packages followed by restarting Rstudio. I am unable to resolve this issue.
Is anyone else facing the same problem or can suggest a solution? Please help me out here.
Regards,
Poojitha Rajasekar
If you want to respond to an answer, please use the ADD COMMENT button and type in the box that appears. The Add your answer box below is for adding answers, not additional questions.
In addition, I requested your sessionInfo() output, which you did not supply. The reason we ask for sessionInfo output is because mis-matched package versions are a major reason for people getting errors. If you want help you have to actually read and respond to my requests!
It's also helpful if you give a small, reproducible example that people can use to test. An example of what I mean follows. As you can see, this works for me, so it's possible you have mis-matched packages.
> library(IlluminaHumanMethylation450kanno.ilmn12.hg19) > library(minfi) > library(DMRcate) > library("CopyNumber450kData") > data(RGcontrolSetEx) > z <- preprocessFunnorm(RGcontrolSetEx) [preprocessFunnorm] Background and dye bias correction with noob [preprocessNoob] Applying R/G ratio flip to fix dye bias... [preprocessFunnorm] Mapping to genome [preprocessFunnorm] Quantile extraction [preprocessFunnorm] Normalization > zz <- cpg.annotate("array",z, "M", "450K", "differential", model.matrix(~factor(rep(1:2, each=26))), coef=2) Your contrast returned 37708 individually significant probes. We recommend the default setting of pcutoff in dmrcate(). > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 14393) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines stats4 parallel stats graphics grDevices utils [8] datasets methods baseI had too many characters, so here's the rest of my sessionInfo()
Sorry about that ! I compared my sessionInfo() with yours. The versions of DMRcate and annotation packages for 450K are the same. However, I have installed R3.3.3. Please see the sessionInfo() on my RStudio in the next comment. However, without making any changes, DMRcate worked for 450K data today. But, it still does not work for EPIC data. This is a bit strange. It still gives the same error.
library(DMRcate)
> library(minfi)
> library(IlluminaHumanMethylationEPICanno.ilm10b2.hg19))
> type<-factor(targets.controlvs3D7D$groups1)
> design<- model.matrix(~type)
> myannotation <- cpg.annotate("array", M.controlvs3D7D, what="M", arraytype = "EPIC",
+ analysis.type="differential", design=design, coef=2)
Error in get(ann) :
cannot open file '~/R/win-library/3.3/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.ilmn12.hg19/data/Rdata.rdb': No such file or directory
In addition: Warning message:
In get(results[[i]], pos = which(search() == packages[[i]])) :
restarting interrupted promise evaluation
Regards,
Poojitha
Here is my session Info:
sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] splines parallel stats4 stats graphics grDevices utils datasets
[9] methods base
other attached packages:
[1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[2] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[3] DMRcate_1.10.7
[4] DMRcatedata_1.10.1
[5] DSS_2.14.0
[6] bsseq_1.10.0
[7] limma_3.30.12
[8] minfi_1.20.2
[9] bumphunter_1.14.0
[10] locfit_1.5-9.1
[11] iterators_1.0.8
[12] foreach_1.4.3
[13] Biostrings_2.42.1
[14] XVector_0.14.0
[15] SummarizedExperiment_1.4.0
[16] Biobase_2.34.0
[17] GenomicRanges_1.26.3
[18] GenomeInfoDb_1.10.3
[19] IRanges_2.8.1
[20] S4Vectors_0.12.1
[21] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] colorspace_1.3-2 siggenes_1.48.0
[3] mclust_5.2.3 biovizBase_1.22.0
[5] htmlTable_1.9 base64enc_0.1-3
[7] dichromat_2.0-0 base64_2.0
[9] interactiveDisplayBase_1.12.0 AnnotationDbi_1.36.2
[11] codetools_0.2-15 R.methodsS3_1.7.1
[13] methylumi_2.20.0 knitr_1.15.1
[15] Formula_1.2-1 Rsamtools_1.26.1
[17] annotate_1.52.1 GO.db_3.4.0
[19] cluster_2.0.5 R.oo_1.21.0
[21] shiny_1.0.0 httr_1.2.1
[23] backports_1.0.5 assertthat_0.1
[25] Matrix_1.2-8 lazyeval_0.2.0
[27] acepack_1.4.1 htmltools_0.3.5
[29] tools_3.3.3 gtable_0.2.0
[31] doRNG_1.6 Rcpp_0.12.9
[33] multtest_2.30.0 preprocessCore_1.36.0
[35] nlme_3.1-131 rtracklayer_1.34.2
[37] stringr_1.2.0 mime_0.5
[39] ensembldb_1.6.2 rngtools_1.2.4
[41] gtools_3.5.0 statmod_1.4.29
[43] XML_3.98-1.5 beanplot_1.2
[45] org.Hs.eg.db_3.4.0 AnnotationHub_2.6.4
[47] zlibbioc_1.20.0 MASS_7.3-45
[49] scales_0.4.1 BSgenome_1.42.0
[51] VariantAnnotation_1.20.2 BiocInstaller_1.24.0
[53] GEOquery_2.40.0 RColorBrewer_1.1-2
[55] missMethyl_1.8.0 yaml_2.1.14
There must be something wrong with the annotation slot for your M.controlvs3D7D object, because cpg.annotate is looking in the wrong place:
If you do
path.package("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")it should return something like
Which is the name of the package. You seem to have some concatenation of the two Illumina methylation annotation packages, which is messing everything up.