Question: How do I get gene annotation for probes on Illumina's HM450k arrays in FDb.InfiniumMethylation.hg19?
1
gravatar for biohack92
4.9 years ago by
biohack92150
United States
biohack92150 wrote:

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?

ADD COMMENTlink modified 4.9 years ago by Neilfws48k • written 4.9 years ago by biohack92150
3
gravatar for Neilfws
4.9 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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"
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Neilfws48k
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