Retrieve annotations for HumanMethylation27 or HumanMethylation450 chips

Description

FDb.InfiniumMethylation.hg19 is an omnibus package that merges all of the existing Illumina Infinium DNA methylation probe annotations into one FDb. However, most users will be analyzing one of the two chips at any given time. The utility functions getPlatform(platform), get450k(), and get27k() retrieve a compact GenomicRanges form of the annotations for the requested platform.

Author(s)

Tim Triche, Jr.

Examples

  hm450.hg18 <- getPlatform(platform='HM450', genome='hg18')
  show(hm450.hg18)

  hm27.hg18 <- get27k(genome='hg18')
  genome(hm27.hg18)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(FDb.InfiniumMethylation.hg18)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: TxDb.Hsapiens.UCSC.hg18.knownGene
Loading required package: org.Hs.eg.db

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/FDb.InfiniumMethylation.hg18/getPlatform.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getPlatform
> ### Title: Retrieve annotations for HumanMethylation27 or
> ###   HumanMethylation450 chips
> ### Aliases: getPlatform get450k get27k
> 
> ### ** Examples
> 
> 
>   hm450.hg18 <- getPlatform(platform='HM450', genome='hg18')
Fetching coordinates for hg18...
>   show(hm450.hg18)
GRanges object with 485517 ranges and 10 metadata columns:
             seqnames               ranges strand |    addressA    addressB
                <Rle>            <IRanges>  <Rle> | <character> <character>
  cg04913815    chr16       [  438,   439]      * |    24771476            
  cg01686861    chr16       [  748,   749]      * |    36644319    45624454
  cg05558259    chr16       [ 1085,  1086]      * |    65765435            
  cg26978960    chr16       [ 2460,  2461]      * |    28717484            
  cg03792876    chr16       [13243, 13244]      * |    42725455            
         ...      ...                  ...    ... .         ...         ...
  cg17939569     chrY [25418818, 25418819]      * |    73757458            
  cg13365400     chrY [25619722, 25619723]      * |    61745505            
  cg21106100     chrY [26964924, 26964925]      * |    56793430            
  cg08265308     chrY [26964938, 26964939]      * |    67794346    26610401
  cg14273923     chrY [26965300, 26965301]      * |    16749405            
             channel platform percentGC               sourceSeq probeType
               <Rle>    <Rle> <numeric>          <DNAStringSet>     <Rle>
  cg04913815    Both    HM450      0.58 TTTCGGTGGT...GTCAGACCCG        cg
  cg01686861     Red    HM450      0.76 CGCCCCCAGG...CACGCCCCCC        cg
  cg05558259    Both    HM450      0.56 CAGCTAGGGA...TGGCAGCACG        cg
  cg26978960    Both    HM450      0.66 CGGCCCAGTA...CTGTCGACTC        cg
  cg03792876    Both    HM450      0.64 ATGGAGGCTT...GCAGGTTACG        cg
         ...     ...      ...       ...                     ...       ...
  cg17939569    Both    HM450      0.42 CGCCTAAATA...AAATCACCGG        cg
  cg13365400    Both    HM450      0.44 CGTCACCTGG...CCCTAAGGAC        cg
  cg21106100    Both    HM450      0.66 CGGATCTTTC...CTGGCCTCCC        cg
  cg08265308     Red    HM450      0.68 CGGCTCCCAA...CATCTTGGCC        cg
  cg14273923    Both    HM450      0.48 TGGTATTGGT...ATAATCGTCG        cg
              probeStart    probeEnd probeTarget
             <character> <character>   <numeric>
  cg04913815         438         487         438
  cg01686861         700         749         748
  cg05558259        1037        1086        1085
  cg26978960        2412        2461        2460
  cg03792876       13195       13244       13243
         ...         ...         ...         ...
  cg17939569    25418818    25418867    25418818
  cg13365400    25619722    25619771    25619722
  cg21106100    26964876    26964925    26964924
  cg08265308    26964890    26964939    26964938
  cg14273923    26965300    26965349    26965300
  -------
  seqinfo: 24 sequences from hg18 genome
> 
>   hm27.hg18 <- get27k(genome='hg18')
Fetching coordinates for hg18...
>   genome(hm27.hg18)
  chr1   chr2   chr3   chr4   chr5   chr6   chr7   chr8   chr9  chr10  chr11 
"hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" 
 chr12  chr13  chr14  chr15  chr16  chr17  chr18  chr19  chr20  chr21  chr22 
"hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" "hg18" 
  chrX   chrY 
"hg18" "hg18" 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>