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Question: Gage package; go.gset() function error: argument "go_id" is missing
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gravatar for Miskey, Csaba
6 days ago by
Germany
Miskey, Csaba20 wrote:

Dear All,

The go.gsets function of gage send the following error:

 go.hs <- go.gsets(species="human")

Gene ID type for 'human' is: 'EG'
Error in initialize(value, ...) :
  argument "go_id" is missing, with no default

Where should the 'go_id' argument be specified?

kg.hsa <- kegg.gsets(species = "hsa", id.type = "kegg")

runs without an error.

Many thanks!
Csaba

>sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

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

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

other attached packages:
 [1] gageData_2.14.0      GO.db_3.4.1          org.Hs.eg.db_3.4.1   AnnotationDbi_1.38.2 IRanges_2.10.5      
 [6] S4Vectors_0.14.7     Biobase_2.36.2       BiocGenerics_0.22.1  BiocInstaller_1.26.1 gage_2.26.3         

loaded via a namespace (and not attached):
 [1] graph_1.54.0      Rcpp_0.12.16      XVector_0.16.0    zlibbioc_1.22.0   bit_1.1-12        R6_2.2.2         
 [7] blob_1.1.1        httr_1.3.1        tools_3.4.4       png_0.1-7         DBI_1.0.0         bit64_0.9-7      
[13] digest_0.6.15     curl_2.8.1        KEGGREST_1.16.1   memoise_1.1.0     RSQLite_2.1.1     compiler_3.4.4   
[19] Biostrings_2.44.2 pkgconfig_2.0.1 

ADD COMMENTlink modified 6 days ago by James W. MacDonald46k • written 6 days ago by Miskey, Csaba20
3
gravatar for James W. MacDonald
6 days ago by
United States
James W. MacDonald46k wrote:

The version of R/Bioconductor you are using is old and no longer supported. This function works for me in a current install. If you still have a problem after upgrading, please let us know.

> z <- go.gsets()
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: stats4
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, sd, var, xtabs

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

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

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: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Gene ID type for 'human' is: 'EG'

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] GO.db_3.6.0          org.Hs.eg.db_3.6.0   AnnotationDbi_1.42.0
[4] IRanges_2.14.1       S4Vectors_0.18.1     Biobase_2.40.0      
[7] BiocGenerics_0.26.0  gage_2.30.0          BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] graph_1.58.0      Rcpp_0.12.16      XVector_0.20.0    zlibbioc_1.26.0  
 [5] bit_1.1-12        R6_2.2.2          blob_1.1.1        httr_1.3.1       
 [9] tools_3.5.0       png_0.1-7         DBI_1.0.0         bit64_0.9-7      
[13] digest_0.6.15     KEGGREST_1.20.0   memoise_1.1.0     RSQLite_2.1.0    
[17] compiler_3.5.0    Biostrings_2.48.0 pkgconfig_2.0.1 
ADD COMMENTlink written 6 days ago by James W. MacDonald46k

I should have checked. Many thanks!
 

ADD REPLYlink written 6 days ago by Miskey, Csaba20
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