cobra function missing

[edammer]

cobra() function is not included with NetZooR_1.6.0 package installed from Bioconductor in R 4.3.1 on WINDOWS:

<...>
batch <- metadata$tcga.cgc_case_batch_number
> length(unique(batch))
[1] 17
> number_of_samples <- dim(gene_expression)[2]
> X <- cbind(rep(1, number_of_samples), as.matrix(dummy_cols(batch)[, -c(1:2)]))
> dim(X)
[1] 572  17
> cobra_estimates <- cobra(X, gene_expression)
Error in cobra(X, gene_expression) : could not find function "cobra"
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] DESeq2_1.42.1               recount3_1.12.0             SummarizedExperiment_1.32.0 GenomicRanges_1.54.1        GenomeInfoDb_1.38.1         IRanges_2.36.0             
 [7] S4Vectors_0.40.2            MatrixGenerics_1.14.0       matrixStats_1.1.0           netZooR_1.6.0               matrixcalc_1.0-6            yarn_1.28.0                
[13] pandaR_1.34.0               Biobase_2.62.0              BiocGenerics_0.48.1         reticulate_1.31             igraph_2.0.2                fastDummies_1.7.4          

loaded via a namespace (and not attached):
  [1] STRINGdb_2.14.3           fs_1.6.3                  bitops_1.0-7              httr_1.4.6                RColorBrewer_1.1-3        doParallel_1.0.17        
  [7] Rgraphviz_2.46.0          repr_1.1.7                tools_4.3.1               doRNG_1.8.6               backports_1.4.1           utf8_1.2.3               
 [13] R6_2.5.1                  vegan_2.6-8               HDF5Array_1.30.1          mgcv_1.8-42               rhdf5filters_1.14.1       permute_0.9-7            
 [19] withr_2.5.0               prettyunits_1.1.1         base64_2.0.1              preprocessCore_1.64.0     cli_3.6.1                 penalized_0.9-52         
 [25] readr_2.1.5               genefilter_1.84.0         askpass_1.1               Rsamtools_2.18.0          pbdZMQ_0.3-12             siggenes_1.76.0          
 [31] illuminaio_0.44.0         R.utils_2.12.3            AnnotationForge_1.44.0    sessioninfo_1.2.2         scrime_1.3.5              plotrix_3.8-4            
 [37] limma_3.58.1              RSQLite_2.3.3             generics_0.1.3            GOstats_2.68.0            quantro_1.36.0            BiocIO_1.12.0            
 [43] gtools_3.9.5              dplyr_1.1.4               GO.db_3.18.0              Matrix_1.5-4.1            fansi_1.0.4               abind_1.4-5              
 [49] R.methodsS3_1.8.2         lifecycle_1.0.3           yaml_2.3.7                edgeR_4.0.16              gplots_3.1.3.1            rhdf5_2.46.1             
 [55] SparseArray_1.2.4         BiocFileCache_2.10.2      grid_4.3.1                blob_1.2.4                crayon_1.5.2              lattice_0.21-8           
 [61] GenomicFeatures_1.54.4    annotate_1.80.0           KEGGREST_1.42.0           pillar_1.9.0              beanplot_1.3.1            rjson_0.2.21             
 [67] codetools_0.2-19          glue_1.6.2                downloader_0.4            data.table_1.14.8         vctrs_0.6.5               png_0.1-8                
 [73] gtable_0.3.4              assertthat_0.2.1          gsubfn_0.7                cachem_1.0.8              S4Arrays_1.2.1            survival_3.5-5           
 [79] iterators_1.0.14          statmod_1.5.0             nlme_3.1-162              Category_2.68.0           bit64_4.0.5               progress_1.2.2           
 [85] filelock_1.0.3            nor1mix_1.3-3             KernSmooth_2.23-21        colorspace_2.1-0          DBI_1.1.3                 nnet_7.3-19              
 [91] tidyselect_1.2.1          bit_4.0.5                 compiler_4.3.1            curl_5.2.1                chron_2.3-61              graph_1.80.0             
 [97] xml2_1.3.5                ggdendro_0.2.0            DelayedArray_0.28.0       rtracklayer_1.62.0        scales_1.3.0              caTools_1.18.2           
[103] hexbin_1.28.4             quadprog_1.5-8            RBGL_1.78.0               rappdirs_0.3.3            stringr_1.5.1             digest_0.6.33            
[109] GEOquery_2.70.0           XVector_0.42.0            htmltools_0.5.5           pkgconfig_2.0.3           base64enc_0.1-3           sparseMatrixStats_1.14.0 
[115] dbplyr_2.5.0              fastmap_1.1.1             rlang_1.1.1               DelayedMatrixStats_1.24.0 jsonlite_1.8.7            BiocParallel_1.36.0      
[121] mclust_6.1.1              R.oo_1.25.0               RCurl_1.98-1.13           magrittr_2.0.3            GenomeInfoDbData_1.2.11   Rhdf5lib_1.24.2          
[127] IRkernel_1.3.2            munsell_0.5.0             Rcpp_1.0.11               proto_1.0.0               sqldf_0.4-11              stringi_1.7.12           
[133] RJSONIO_1.3-1.9           zlibbioc_1.48.0           MASS_7.3-60               plyr_1.8.9                bumphunter_1.44.0         org.Hs.eg.db_3.18.0      
[139] minfi_1.48.0              parallel_4.3.1            Biostrings_2.70.1         IRdisplay_1.1             splines_4.3.1             multtest_2.58.0          
[145] hash_2.2.6.3              hms_1.1.3                 locfit_1.5-9.10           uuid_1.2-1                RUnit_0.4.33              base64url_1.4            
[151] rngtools_1.5.2            reshape2_1.4.4            biomaRt_2.58.2            XML_3.99-0.17             evaluate_0.21             BiocManager_1.30.22      
[157] tzdb_0.4.0                foreach_1.5.2             tidyr_1.3.1               openssl_2.1.0             purrr_1.0.1               reshape_0.8.9            
[163] ggplot2_3.4.4             xtable_1.8-4              restfulr_0.0.15           viridisLite_0.4.2         RCy3_2.22.1               tibble_3.2.1             
[169] memoise_2.0.1             AnnotationDbi_1.64.1      GenomicAlignments_1.38.2  cluster_2.1.4             GSEABase_1.64.0 

[taraeicher]

Thank you for raising this issue. The latest Bioconductor release was made prior to the integration of COBRA. To use COBRA, you can install the latest version of netZooR from GitHub using the following command: remotes::install_github("netZoo/netZooR@devel")

[taraeicher]

@edammer Please let us know whether this issue has been resolved.