RnBeads::combine() - error?
1
0
Entering edit mode
D • 0
@d-16116
Last seen 19 months ago
UK

Dear all,

I have datasets from both EPIC and 450k, I am trying to use the RnBeads combine function to combine them into a single object.

This is example code from this tutorial, applied to the data provided in the tutorial: https://rnbeads.org/materials/data/tutorial/cross_platform/tutorial.html

When I run the following code, I get an error:

################ combine EPIC and 450k ##############
DIR_DATASETS<-"~/Downloads/"
# Let us now load each individual RnBSet object:

PLATFORMS<-c("450k", "EPIC")

rnb.sets<-list()
for(pl in PLATFORMS){

  dfile<-sprintf("dataset-%s.zip", pl)

  rnb.sets[[pl]]<-load.rnb.set(file.path(DIR_DATASETS, dfile))

}
> rnb.set.arrays<-combine(rnb.sets[["450k"]], rnb.sets[["EPIC"]], type="common")
Error in do.call(combine, list(y, ...)) : 
  argument "y" is missing, with no default

The same error happens with my own data (RnBeadRawSet). I don't get a combined RnBeadRawSet object out of either the tutorial or my own data. Is this a bug or am I using it wrong?

Thanks in advance!

R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] LOLA_1.14.0                             GLAD_2.48.0                             RnBeads.hg38_1.16.0                    
 [4] GOstats_2.50.0                          graph_1.62.0                            Category_2.50.0                        
 [7] Matrix_1.2-18                           RnBeads_2.5.0                           plyr_1.8.6                             
[10] methylumi_2.30.0                        minfi_1.30.0                            bumphunter_1.26.0                      
[13] locfit_1.5-9.4                          iterators_1.0.12                        foreach_1.5.0                          
[16] Biostrings_2.52.0                       XVector_0.24.0                          SummarizedExperiment_1.14.1            
[19] DelayedArray_0.10.0                     BiocParallel_1.18.1                     FDb.InfiniumMethylation.hg19_2.2.0     
[22] org.Hs.eg.db_3.8.2                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.36.4                 
[25] AnnotationDbi_1.46.1                    reshape2_1.4.4                          scales_1.1.1                           
[28] Biobase_2.44.0                          illuminaio_0.26.0                       matrixStats_0.56.0                     
[31] limma_3.40.6                            gridExtra_2.3                           gplots_3.0.3                           
[34] ggplot2_3.3.1                           fields_10.3                             maps_3.3.0                             
[37] spam_2.5-1                              dotCall64_1.0-0                         ff_2.2-14.2                            
[40] bit_1.1-15.2                            cluster_2.1.0                           MASS_7.3-51.6                          
[43] GenomicRanges_1.36.1                    GenomeInfoDb_1.20.0                     IRanges_2.18.3                         
[46] S4Vectors_0.22.1                        BiocGenerics_0.30.0                    

loaded via a namespace (and not attached):
  [1] backports_1.1.7          GSEABase_1.46.0          splines_3.6.3            sva_3.32.1               digest_0.6.25           
  [6] GO.db_3.8.2              gdata_2.18.0             fansi_0.4.1              magrittr_1.5             memoise_1.1.0           
 [11] remotes_2.1.1            readr_1.3.1              annotate_1.62.0          askpass_1.1              siggenes_1.58.0         
 [16] prettyunits_1.1.1        colorspace_1.4-1         blob_1.2.1               dplyr_1.0.0              callr_3.4.3             
 [21] crayon_1.3.4             RCurl_1.98-1.2           genefilter_1.66.0        GEOquery_2.52.0          survival_3.1-12         
 [26] glue_1.4.1               gtable_0.3.0             zlibbioc_1.30.0          pkgbuild_1.0.8           Rgraphviz_2.28.0        
 [31] Rhdf5lib_1.6.3           HDF5Array_1.12.3         DBI_1.1.0                rngtools_1.5             Rcpp_1.0.4.6            
 [36] xtable_1.8-4             progress_1.2.2           mclust_5.4.6             preprocessCore_1.46.0    AnnotationForge_1.26.0  
 [41] httr_1.4.1               RColorBrewer_1.1-2       ellipsis_0.3.1           pkgconfig_2.0.3          reshape_0.8.8           
 [46] XML_3.99-0.3             tidyselect_1.1.0         rlang_0.4.6              munsell_0.5.0            tools_3.6.3             
 [51] cli_2.0.2                generics_0.0.2           RSQLite_2.2.0            stringr_1.4.0            yaml_2.2.1              
 [56] processx_3.4.2           bit64_0.9-7              beanplot_1.2             caTools_1.18.0           scrime_1.3.5            
 [61] purrr_0.3.4              RBGL_1.60.0              nlme_3.1-147             doRNG_1.8.2              nor1mix_1.3-0           
 [66] xml2_1.3.2               biomaRt_2.40.5           compiler_3.6.3           rstudioapi_0.11          curl_4.3                
 [71] tibble_3.0.1             stringi_1.4.6            ps_1.3.3                 lattice_0.20-41          multtest_2.40.0         
 [76] vctrs_0.3.1              pillar_1.4.4             lifecycle_0.2.0          BiocManager_1.30.10      data.table_1.12.8       
 [81] bitops_1.0-6             rtracklayer_1.44.4       R6_2.4.1                 KernSmooth_2.23-17       codetools_0.2-16        
 [86] gtools_3.8.2             assertthat_0.2.1         rhdf5_2.28.1             openssl_1.4.1            rprojroot_1.3-2         
 [91] withr_2.2.0              GenomicAlignments_1.20.1 Rsamtools_2.0.3          GenomeInfoDbData_1.2.1   mgcv_1.8-31             
 [96] hms_0.5.3                quadprog_1.5-8           tidyr_1.1.0              base64_2.0               DelayedMatrixStats_1.6.1

EDIT:

Hi all,

To rule out old packages I have updated R, bioconductor and Rnbeads to newest versions. Issue appears to be the same:

> DIR_DATASETS<-"~/Downloads/"
> PLATFORMS<-c("450k", "EPIC")
> rnb.sets<-list()
> for(pl in PLATFORMS){
+   
+   dfile<-sprintf("dataset-%s.zip", pl)
+   
+   rnb.sets[[pl]]<-load.rnb.set(file.path(DIR_DATASETS, dfile))
+   
+ }
> rnb.set.arrays<-combine(rnb.sets[["450k"]], rnb.sets[["EPIC"]], type="common")
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'y' in selecting a method for function 'combine': error in evaluating the argument 'y' in selecting a method for function 'combine': error in evaluating the argument 'args' in selecting a method for function 'do.call': argument "y" is missing, with no default

EDIT2: It seems to run when type isn't set at all. Setting it to anything causes the error code above. It is currently running, albeit with the default type (all) which seems to be inappropriate.

rnb.set.arrays<-combine(rnb.sets[["450k"]], rnb.sets[["EPIC"]])

Bug?

> sessionInfo()
R version 4.0.1 (2020-06-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] IlluminaHumanMethylationEPICmanifest_0.3.0 IlluminaHumanMethylation450kmanifest_0.4.0 doParallel_1.0.15                         
 [4] LOLA_1.18.0                                GLAD_2.52.0                                RnBeads.hg38_1.20.0                       
 [7] GOstats_2.54.0                             graph_1.66.0                               Category_2.54.0                           
[10] Matrix_1.2-18                              RnBeads.hg19_1.20.0                        RnBeads_2.6.0                             
[13] plyr_1.8.6                                 methylumi_2.34.0                           minfi_1.34.0                              
[16] bumphunter_1.30.0                          locfit_1.5-9.4                             iterators_1.0.12                          
[19] foreach_1.5.0                              Biostrings_2.56.0                          XVector_0.28.0                            
[22] SummarizedExperiment_1.18.1                DelayedArray_0.14.0                        FDb.InfiniumMethylation.hg19_2.2.0        
[25] org.Hs.eg.db_3.11.4                        TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2    GenomicFeatures_1.40.0                    
[28] AnnotationDbi_1.50.0                       reshape2_1.4.4                             scales_1.1.1                              
[31] Biobase_2.48.0                             illuminaio_0.30.0                          matrixStats_0.56.0                        
[34] limma_3.44.1                               gridExtra_2.3                              gplots_3.0.3                              
[37] ggplot2_3.3.1                              fields_10.3                                maps_3.3.0                                
[40] spam_2.5-1                                 dotCall64_1.0-0                            ff_2.2-14.2                               
[43] bit_1.1-15.2                               cluster_2.1.0                              MASS_7.3-51.6                             
[46] GenomicRanges_1.40.0                       GenomeInfoDb_1.24.0                        IRanges_2.22.2                            
[49] S4Vectors_0.26.1                           BiocGenerics_0.34.0                       

loaded via a namespace (and not attached):
 [1] BiocFileCache_1.12.0      GSEABase_1.50.1           splines_4.0.1             BiocParallel_1.22.0       digest_0.6.25            
 [6] GO.db_3.11.4              gdata_2.18.0              magrittr_1.5              memoise_1.1.0             readr_1.3.1              
[11] annotate_1.66.0           askpass_1.1               siggenes_1.62.0           prettyunits_1.1.1         colorspace_1.4-1         
[16] blob_1.2.1                rappdirs_0.3.1            dplyr_1.0.0               crayon_1.3.4              RCurl_1.98-1.2           
[21] genefilter_1.70.0         GEOquery_2.56.0           survival_3.1-12           glue_1.4.1                gtable_0.3.0             
[26] zlibbioc_1.34.0           Rgraphviz_2.32.0          Rhdf5lib_1.10.0           HDF5Array_1.16.0          DBI_1.1.0                
[31] rngtools_1.5              Rcpp_1.0.4.6              xtable_1.8-4              progress_1.2.2            mclust_5.4.6             
[36] preprocessCore_1.50.0     AnnotationForge_1.30.1    httr_1.4.1                RColorBrewer_1.1-2        ellipsis_0.3.1           
[41] farver_2.0.3              pkgconfig_2.0.3           reshape_0.8.8             XML_3.99-0.3              dbplyr_1.4.4             
[46] labeling_0.3              tidyselect_1.1.0          rlang_0.4.6               munsell_0.5.0             tools_4.0.1              
[51] generics_0.0.2            RSQLite_2.2.0             stringr_1.4.0             bit64_0.9-7               beanplot_1.2             
[56] caTools_1.18.0            scrime_1.3.5              purrr_0.3.4               RBGL_1.64.0               nlme_3.1-147             
[61] doRNG_1.8.2               nor1mix_1.3-0             xml2_1.3.2                biomaRt_2.44.0            compiler_4.0.1           
[66] rstudioapi_0.11           curl_4.3                  tibble_3.0.1              stringi_1.4.6             lattice_0.20-41          
[71] multtest_2.44.0           vctrs_0.3.1               pillar_1.4.4              lifecycle_0.2.0           BiocManager_1.30.10      
[76] data.table_1.12.8         bitops_1.0-6              rtracklayer_1.48.0        R6_2.4.1                  KernSmooth_2.23-17       
[81] codetools_0.2-16          gtools_3.8.2              assertthat_0.2.1          rhdf5_2.32.0              openssl_1.4.1            
[86] withr_2.2.0               GenomicAlignments_1.24.0  Rsamtools_2.4.0           GenomeInfoDbData_1.2.3    hms_0.5.3                
[91] quadprog_1.5-8            tidyr_1.1.0               base64_2.0                DelayedMatrixStats_1.10.0
RnBeads Rnbeads2.0 RnBeads2 • 585 views
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2
Entering edit mode
mscherer ▴ 50
@mscherer-19737
Last seen 6 months ago
Spain/Barcelona/Centre for Genomic Regu…

Hi!

This might, indeed, be a bug in the software. I will work on fixing this. However, there should be an easy workaround for you: Instead of using the combine function, you can check out the rnb.combine.arrays, which essentially has the same functionality.

I hope that solves the issue.

Best,

Michael

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0
Entering edit mode

Hi,

It does help when I combine two array data container, but now I want to combine 450K, RRBS and WGBS data, it seem that i came across the same problem as D did, how can i fix this ?

ADD REPLY
0
Entering edit mode

Hi,

For this task, you should first convert the RnBeadSet object into an RnBiseqSet object using the constructor RnBiseqSet. Afterwards, you can use the function combine.

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