Question: IlluminaHumanMethylation450k.db - error on trying to insall
0
gravatar for Brian Smith
3.6 years ago by
Brian Smith120
United States
Brian Smith120 wrote:

Hi,

I was trying to install IlluminaHumanMethylation450k.db with biocLite, but I get an error on trying to install. Is there something else that I need to do?

Details are:

> biocLite("IlluminaHumanMethylation450k.db")

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.0.
Installing package(s) ‘IlluminaHumanMethylation450k.db’
installing the source package ‘IlluminaHumanMethylation450k.db’

trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/IlluminaHumanMethylation450k.db_2.0.9.tar.gz'
Content type 'application/x-gzip' length 63268317 bytes (60.3 MB)
==================================================
downloaded 60.3 MB

* installing *source* package ‘IlluminaHumanMethylation450k.db’ ...

.

.

.

Warning in .recacheSubclasses(def@className, def, doSubclasses, env) :
  undefined subclass "externalRefMethod" of class "functionORNULL"; definition not updated
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
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IlluminaHumanMethylation450k.db’

 

 

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] FDb.InfiniumMethylation.hg19_2.2.0                 org.Hs.eg.db_3.1.2                                 RSQLite_1.0.0                                     
 [4] DBI_0.3.1                                          TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2            GenomicFeatures_1.20.6                            
 [7] AnnotationDbi_1.30.1                               IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 IlluminaHumanMethylation450kmanifest_0.4.0        
[10] minfi_1.14.0                                       bumphunter_1.8.0                                   locfit_1.5-9.1                                    
[13] iterators_1.0.8                                    foreach_1.4.3                                      Biostrings_2.36.4                                 
[16] XVector_0.8.0                                      lattice_0.20-33                                    Biobase_2.28.0                                    
[19] DESeq2_1.8.2                                       RcppArmadillo_0.6.100.0.0                          Rcpp_0.12.1                                       
[22] GenomicRanges_1.20.8                               GenomeInfoDb_1.4.3                                 IRanges_2.2.9                                     
[25] S4Vectors_0.6.6                                    BiocGenerics_0.14.0                                BiocInstaller_1.18.5                              

loaded via a namespace (and not attached):
 [1] nor1mix_1.2-1           splines_3.2.0           Formula_1.2-1           latticeExtra_0.6-26     doRNG_1.6               Rsamtools_1.20.5       
 [7] quadprog_1.5-5          limma_3.24.15           digest_0.6.8            RColorBrewer_1.1-2      colorspace_1.2-6        preprocessCore_1.30.0  
[13] plyr_1.8.3              GEOquery_2.34.0         siggenes_1.42.0         XML_3.98-1.3            biomaRt_2.24.1          genefilter_1.50.0      
[19] zlibbioc_1.14.0         xtable_1.7-4            scales_0.3.0            BiocParallel_1.2.22     annotate_1.46.1         beanplot_1.2           
[25] pkgmaker_0.22           ggplot2_1.0.1           nnet_7.3-11             proto_0.3-10            survival_2.38-3         magrittr_1.5           
[31] mclust_5.0.2            nlme_3.1-122            MASS_7.3-44             foreign_0.8-66          tools_3.2.0             registry_0.3           
[37] matrixStats_0.14.2      stringr_1.0.0           munsell_0.4.2           cluster_2.0.3           rngtools_1.2.4          base64_1.1             
[43] lambda.r_1.1.7          futile.logger_1.4.1     grid_3.2.0              RCurl_1.95-4.7          bitops_1.0-6            gtable_0.1.2           
[49] codetools_0.2-14        multtest_2.24.0         reshape_0.8.5           reshape2_1.4.1          illuminaio_0.10.0       GenomicAlignments_1.4.2
[55] gridExtra_2.0.0         rtracklayer_1.28.10     Hmisc_3.17-0            futile.options_1.0.0    stringi_0.5-5           geneplotter_1.46.0     
[61] rpart_4.1-10            acepack_1.3-3.3   

 

thanks!!

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Brian Smith120
Answer: IlluminaHumanMethylation450k.db - error on trying to insall
0
gravatar for James W. MacDonald
3.6 years ago by
United States
James W. MacDonald50k wrote:

You should probably follow the recommendations given during the package install and use the FDb.InfiniumMethylation.hg19 package instead. The package you are attempting to install was deprecated (IIRC) two releases ago, in favor of the FDb versions.

ADD COMMENTlink written 3.6 years ago by James W. MacDonald50k
Answer: IlluminaHumanMethylation450k.db - error on trying to insall
0
gravatar for Brian Smith
3.6 years ago by
Brian Smith120
United States
Brian Smith120 wrote:

James,

I was trying to use some of the functions in the IlluminaHumanMethylation450k.db package (e.g.IlluminaHumanMethylation450kALIAS2PROBE) that don't appear to be in the FDb.InfiniumMethylation.hg19 documentation. Is there a way that I can get gene to probe information in the new (or another) package?

thanks!

ADD COMMENTlink written 3.6 years ago by Brian Smith120

The FDb packages are more modern in a lot of ways, but that means you need to know something about things like GRanges, etc.

> z <- get450k()
Fetching coordinates for hg19...
> z
GRanges object with 485577 ranges and 10 metadata columns:
             seqnames               ranges strand   |    addressA    addressB
                <Rle>            <IRanges>  <Rle>   | <character> <character>
  cg04913815    chr16       [60438, 60439]      *   |    24771476            
  cg01686861    chr16       [60748, 60749]      *   |    36644319    45624454
  cg05558259    chr16       [61085, 61086]      *   |    65765435            
  cg26978960    chr16       [62460, 62461]      *   |    28717484            
  cg03792876    chr16       [73243, 73244]      *   |    42725455            
         ...      ...                  ...    ... ...         ...         ...
  cg17939569     chrY [27009430, 27009431]      *   |    73757458            
  cg13365400     chrY [27210334, 27210335]      *   |    61745505            
  cg21106100     chrY [28555536, 28555537]      *   |    56793430            
  cg08265308     chrY [28555550, 28555551]      *   |    67794346    26610401
  cg14273923     chrY [28555912, 28555913]      *   |    16749405    

<snip>

> getNearestGene(z[1:5,])
           queryHits subjectHits distance nearestGeneSymbol
cg04913815         1         666     1115          DDX11L10
cg01686861         2         666      805          DDX11L10
cg05558259         3         666      468          DDX11L10
cg26978960         4         666        0          DDX11L10
cg03792876         5         666     9152          DDX11L10

> getNearestTSS(z[1:5,])
           queryHits subjectHits distance nearestGeneSymbol nearestTranscript
cg04913815         1         799     1115          DDX11L10        uc010bqm.2
cg01686861         2         799      805          DDX11L10        uc010bqm.2
cg05558259         3         799      468          DDX11L10        uc010bqm.2
cg26978960         4         799      904          DDX11L10        uc010bqm.2
cg03792876         5         799    11687          DDX11L10        uc010bqm.2

Does that help?

 

ADD REPLYlink written 3.6 years ago by James W. MacDonald50k

Well, it helps because now I need to understand GRanges ;)

 

ADD REPLYlink written 3.6 years ago by Brian Smith120
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