I am trying to install IlluminaHumanMethylation450k.db but can't manage to do so:
Error : .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation450k.db', details: call: NULL error: 'fun' is defunct. Use 'FDb.InfiniumMethylation.hg19' instead. Use 'FDb.InfiniumMethylation.hg18' instead. Use 'mapToGenome() function in minfi or methylumi' instead. See help("Defunct") Error: loading failed Execution halted ERROR: loading failed
I know the package is deprecated. What I wanted to use is the function to map 450K probes to ensembl gene ids (GRCh37) which had been previously done using that package in our study, and for consisteny reasons I would need the same mapping again.
I could not find a way to get this mapping with mapToGenome() or FDb.InfiniumMethylation.hg19, but if there is a way I am not aware of, please tell me.
Otherwise, if anybody knows what to do to get IlluminaHumanMethylation450k.db working again, I would be very happy. I've tried for many hours since yesterday without success. Solutions like in ‘IlluminaHumanMethylation450k.db’ had non-zero exit status did also not help, as here the error is a different one, but I can't find out how to solve it.
> sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Gentoo/Linux locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8  LC_MESSAGES=C LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached):  tools_3.2.2