Question: Importing Infinium data files using RnBeads::rnb.execute.import()
0
gravatar for Habil Zare
2.9 years ago by
Habil Zare170
United States/Austin Area
Habil Zare170 wrote:

I cannot import beta values using the rnb.execute.import function from the RnBeads package:

rnb.execute.import(data.source=c("annotation"=clinicalFile,"beta"=dnamCsvFile), data.type="infinium.data.files",verbose=TRUE)

2016-12-06 10:49:24     3.2  STATUS                                         STARTED Loading Data from Table Files

2016-12-06 10:49:25     3.2 WARNING                                             The sample sheet table has only one column. Please check import.table.separator option

2016-12-06 10:49:26     3.2    INFO                                             Read table with sample information

2016-12-06 10:49:27     3.2    INFO                                             Read table with betas

Error in rnb.get.annotation(target, assembly) : unsupported assembly

In addition: Warning message:

In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :

  there is no package called ‘RnBeads.h19’

Why do I get this error although I have installed RnBeads.hg19 and RnBeads knows this too, i.e.,:

res <- rnb.get.annotation("promoters",assembly="hg19")
class(res)
[1] "GRangesList"
attr(,"package")
[1] "GenomicRanges"

sessionInfo()

R version 3.3.2 (2016-10-31)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X Mavericks 10.9.5


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] grid      stats4    parallel  stats     graphics  grDevices utils    

 [8] datasets  methods   base     


other attached packages:

 [1] RnBeads.hg19_1.6.0                     

 [2] RnBeads_1.6.1                          

 [3] plyr_1.8.4                             

 [4] methylumi_2.20.0                       

 [5] minfi_1.20.0                           

 [6] bumphunter_1.14.0                      

 [7] locfit_1.5-9.1                         

 [8] iterators_1.0.8                        

 [9] foreach_1.4.3                          

[10] Biostrings_2.42.1                      

[11] XVector_0.14.0                         

[12] SummarizedExperiment_1.4.0             

[13] FDb.InfiniumMethylation.hg19_2.2.0     

[14] org.Hs.eg.db_3.4.0                     

[15] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2

[16] GenomicFeatures_1.26.0                 

[17] AnnotationDbi_1.36.0                   

[18] reshape2_1.4.2                         

[19] scales_0.4.1                           

[20] Biobase_2.34.0                         

[21] illuminaio_0.16.0                      

[22] matrixStats_0.51.0                     

[23] limma_3.30.6                           

[24] gridExtra_2.2.1                        

[25] gplots_3.0.1                           

[26] ggplot2_2.2.0                          

[27] fields_8.4-1                           

[28] maps_3.1.1                             

[29] spam_1.4-0                             

[30] ff_2.2-13                              

[31] bit_1.1-12                             

[32] cluster_2.0.5                          

[33] RColorBrewer_1.1-2                     

[34] MASS_7.3-45                            

[35] GenomicRanges_1.26.1                   

[36] GenomeInfoDb_1.10.1                    

[37] IRanges_2.8.1                          

[38] S4Vectors_0.12.1                       

[39] BiocGenerics_0.20.0                    


loaded via a namespace (and not attached):

 [1] nlme_3.1-128             bitops_1.0-6             httr_1.2.1              

 [4] tools_3.3.2              doRNG_1.6                nor1mix_1.2-2           

 [7] R6_2.2.0                 KernSmooth_2.23-15       DBI_0.5-1               

[10] lazyeval_0.2.0           colorspace_1.3-1         base64_2.0              

[13] preprocessCore_1.36.0    pkgmaker_0.22            rtracklayer_1.34.1      

[16] caTools_1.17.1           genefilter_1.56.0        quadprog_1.5-5          

[19] stringr_1.1.0            digest_0.6.10            Rsamtools_1.26.1        

[22] siggenes_1.48.0          GEOquery_2.40.0          RSQLite_1.1             

[25] mclust_5.2               BiocParallel_1.8.1       gtools_3.5.0            

[28] RCurl_1.95-4.8           magrittr_1.5             Matrix_1.2-7.1          

[31] Rcpp_0.12.8              munsell_0.4.3            stringi_1.1.2           

[34] zlibbioc_1.20.0          gdata_2.17.0             lattice_0.20-34         

[37] splines_3.3.2            multtest_2.30.0          annotate_1.52.0         

[40] beanplot_1.2             rngtools_1.2.4           codetools_0.2-15        

[43] biomaRt_2.30.0           XML_3.98-1.5             data.table_1.9.8        

[46] gtable_0.2.0             openssl_0.9.5            reshape_0.8.6           

[49] assertthat_0.1           xtable_1.8-2             survival_2.40-1         

[52] tibble_1.2               GenomicAlignments_1.10.0 registry_0.3            

[55] memoise_1.0.0           

 

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