[BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?

[Ed Schwalbe]

> James W. MacDonald <jmacdon at ...> writes:
> You would be better off using the FDb.InfiniumMethylation.hg19 package, 
> which not only has all the locations for the probes, but also has them 
> in a more useful format.
> 
>  > library(FDb.InfiniumMethylation.hg19)
>  > x <- get450k()
> Warning message:
> In if (is.na(genome(GR))) { :
>    the condition has length > 1 and only the first element will be used
>  > x
> GRanges with 485577 ranges and 7 metadata columns:
>               seqnames               ranges strand   | addressA addressB 
> channel
> <Rle> <IRanges> <Rle>   | <Rle> <Rle> <Rle>
>    cg13869341     chr1       [15865, 15866]      *   | 62703328 
> 16661461     Red
>    cg14008030     chr1       [18827, 18828]      *   | 27651330 <NA>    Both
>    cg12045430     chr1       [29407, 29408]      *   | 25703424 
> 34666387     Red
>    cg20826792     chr1       [29425, 29426]      *   | 61731400 
> 14693326     Red
>    cg00381604     chr1       [29435, 29436]      *   | 26752380 
> 50693408     Red

Does anyone know why Jim's lines of code do not work on my R installation
(R3.0.1)?

Many thanks,

Ed

library(FDb.InfiniumMethylation.hg19)
x <- get450k()
Error in `seqinfo<-`(`*tmp*`, value = NULL) : 
  the supplied 'seqinfo' must be a Seqinfo object
In addition: Warning message:
In if (is.na(genome(GR))) { :
  the condition has length > 1 and only the first element will be used

sessionInfo()

R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C           
LC_COLLATE=C         LC_MONETARY=C       
 [6] LC_MESSAGES=C        LC_PAPER=C           LC_NAME=C           
LC_ADDRESS=C         LC_TELEPHONE=C      
[11] LC_MEASUREMENT=C     LC_IDENTIFICATION=C 

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
base     

other attached packages:
 [1] IlluminaHumanMethylation450k.db_2.0.7 org.Hs.eg.db_2.9.0                   
 [3] RSQLite_0.11.4                        DBI_0.2-7                            
 [5] FDb.InfiniumMethylation.hg19_1.0.1    rtracklayer_1.20.2                   
 [7] GenomicFeatures_1.12.2                AnnotationDbi_1.22.6                 
 [9] BiocInstaller_1.10.2                  minfi_1.6.0                          
[11] Biostrings_2.28.0                     GenomicRanges_1.12.4                 
[13] IRanges_1.18.1                        reshape_0.8.4                        
[15] plyr_1.8                              lattice_0.20-15                      
[17] Biobase_2.20.1                        BiocGenerics_0.6.0                   

loaded via a namespace (and not attached):
 [1] BSgenome_1.28.0       MASS_7.3-26           R.methodsS3_1.4.4    
RColorBrewer_1.0-5    RCurl_1.95-4.1       
 [6] Rsamtools_1.12.3      XML_3.98-1.1          beanplot_1.1         
biomaRt_2.16.0        bitops_1.0-5         
[11] grid_3.0.1            illuminaio_0.2.0      limma_3.16.5         
matrixStats_0.8.1     mclust_4.1           
[16] multtest_2.16.0       nor1mix_1.1-4         preprocessCore_1.22.0
siggenes_1.34.0       splines_3.0.1        
[21] stats4_3.0.1          survival_2.37-4       tools_3.0.1          
zlibbioc_1.6.0