How do I get gene annotation for probes on Illumina's HM450k arrays in FDb.InfiniumMethylation.hg19?

Question

[biohack92]

So I used the IlluminaHumanMethylation450k.db annotation package to find the probes associated with particular genes of interest. I sent my code to a colleague, but she received the following warning when loading the annotation package.

    3: 'IlluminaHumanMethylation450k.db' is deprecated.
    Use 'FDb.InfiniumMethylation.hg19' instead.
    Use 'FDb.InfiniumMethylation.hg18' instead.
    Use 'mapToGenome() function in minfi or methylumi' instead.

The 'FDb.InfiniumMethylation.hg19' package doesn't seem to have the gene names associated to each probe, so my question is, can we use the gene-to-probe mapping found in 'IlluminaHumanMethylation450k.db' for the 'FDb.InfiniumMethylation.hg19' annotation?

Answer 1

[Neilfws]

For gene symbol to probe mapping, I'd use the newer annotation package IlluminaHumanMethylation450kanno.ilmn12.hg19.

source("http://bioconductor.org/biocLite.R")
biocLite("IlluminaHumanMethylation450kanno.ilmn12.hg19")
data(IlluminaHumanMethylation450kanno.ilmn12.hg19)

The documentation and methods are not great just now, but you can extract a DataFrame from it like this:

anno <- IlluminaHumanMethylation450kanno.ilmn12.hg19@data$Other
names(anno)

#  [1] "Forward_Sequence"         "SourceSeq"                "Random_Loci"             
#  [4] "Methyl27_Loci"            "UCSC_RefGene_Name"        "UCSC_RefGene_Accession"  
#  [7] "UCSC_RefGene_Group"       "Phantom"                  "DMR"                     
# [10] "Enhancer"                 "HMM_Island"               "Regulatory_Feature_Name" 
# [13] "Regulatory_Feature_Group" "DHS"