Question

STRINGdb string_db$map error

1

Entering edit mode

Jessica ▴ 10

@9faea85b

Last seen 2.7 years ago

United Kingdom

Hello, having a problem with some code which previously worked with version 11 of STRINGdb but now throws an error with version 11.5:

library(STRINGdb)
string_db <- STRINGdb$new(version="11.5", species=9606, score_threshold=150, input_directory=getwd())

symbol <- data.frame(gene=dat$symbol)
string2symbol <- string_db$map(symbol, "gene", takeFirst=F, removeUnmappedRows=F)

Error in `[.data.frame`(x, r, vars, drop = drop) : 
  undefined columns selected

I can potentially work around it using the aliases file from STRINGdb but I'd rather not have to (9606.protein.aliases.v11.5.txt).

Many thanks for any advice.

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /tmp_mnt/filer1/software/R_v4.0.3/lib64/R/lib/libRblas.so
LAPACK: /tmp_mnt/filer1/software/R_v4.0.3/lib64/R/lib/libRlapack.so

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

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

other attached packages:
[1] STRINGdb_2.2.2

loaded via a namespace (and not attached):
 [1] igraph_1.2.6       hash_2.2.6.1       Rcpp_1.0.6         magrittr_2.0.1     bit_4.0.4          rlang_1.0.1        fastmap_1.1.0     
 [8] blob_1.2.1         plyr_1.8.6         caTools_1.18.2     tools_4.0.3        png_0.1-7          plotrix_3.8-1      KernSmooth_2.23-17
[15] cli_2.3.0          DBI_1.1.1          gtools_3.8.2       bit64_4.0.5        assertthat_0.2.1   RColorBrewer_1.1-2 vctrs_0.3.8       
[22] bitops_1.0-6       RCurl_1.98-1.2     cachem_1.0.1       memoise_2.0.0      glue_1.4.2         RSQLite_2.2.3      gsubfn_0.7        
[29] compiler_4.0.3     gplots_3.1.1       chron_2.3-56       sqldf_0.4-11       proto_1.0.0        pkgconfig_2.0.3

STRINGdb HELP • 2.2k views

ADD COMMENT • link updated 21 months ago by Rodrigo ▴ 10 • written 2.7 years ago by Jessica ▴ 10

score 0 · Answer 1 · 2022-02-25

0

Entering edit mode

damian.szk ▴ 110

@damianszk-12963

Last seen 4 months ago

Switzerland

Dear Jessica,

You have an old version of the package. STRING v11.5 is enabled starting from version 2.5 of STRINGdb package. You would need to update bioconductor to download the newest package, or you can do it load it directly from the source.

It should have provided better error message, but we cannot update the code for old packages.

Best, Damian.

ADD COMMENT • link 2.7 years ago damian.szk ▴ 110

0

Entering edit mode

Hi Damian,

Thanks for the package! FYI, I am having the same issue as Jessica while running the same code even with the most recent version of STRINGdb. I also had it with R 4.0.3 and a former version of STRINGdb (2.0.2).

My current sessionInfo():

R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /opt/R/4.2.2/lib/R/lib/libRblas.so
LAPACK: /opt/R/4.2.2/lib/R/lib/libRlapack.so

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

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

other attached packages:
 [1] STRINGdb_2.10.1       org.Mm.eg.db_3.16.0   AnnotationDbi_1.60.0  IRanges_2.32.0        S4Vectors_0.36.1      Biobase_2.58.0        BiocGenerics_0.44.0   clusterProfiler_4.6.0
 [9] ComplexHeatmap_2.14.0 DT_0.27               ggplot2_3.4.0        

loaded via a namespace (and not attached):
  [1] shadowtext_0.1.2       circlize_0.4.15        fastmatch_1.1-3        plyr_1.8.8             igraph_1.3.5           lazyeval_0.2.2         splines_4.2.2          BiocParallel_1.32.5   
  [9] crosstalk_1.2.0        GenomeInfoDb_1.34.9    digest_0.6.31          foreach_1.5.2          yulab.utils_0.0.6      htmltools_0.5.4        GOSemSim_2.24.0        viridis_0.6.2         
 [17] GO.db_3.16.0           fansi_1.0.4            magrittr_2.0.3         memoise_2.0.1          cluster_2.1.4          doParallel_1.0.17      Biostrings_2.66.0      graphlayouts_0.8.4    
 [25] matrixStats_0.63.0     enrichplot_1.18.3      colorspace_2.1-0       blob_1.2.3             ggrepel_0.9.3          xfun_0.37              dplyr_1.1.0            crayon_1.5.2          
 [33] RCurl_1.98-1.10        jsonlite_1.8.4         scatterpie_0.1.8       iterators_1.0.14       ape_5.6-2              glue_1.6.2             hash_2.2.6.2           polyclip_1.10-4       
 [41] gtable_0.3.1           zlibbioc_1.44.0        XVector_0.38.0         GetoptLong_1.0.5       shape_1.4.6            scales_1.2.1           DOSE_3.24.2            DBI_1.1.3             
 [49] Rcpp_1.0.10            plotrix_3.8-2          viridisLite_0.4.1      clue_0.3-64            gridGraphics_0.5-1     tidytree_0.4.2         bit_4.0.5              sqldf_0.4-11          
 [57] htmlwidgets_1.6.1      httr_1.4.4             fgsea_1.24.0           gplots_3.1.3           RColorBrewer_1.1-3     ellipsis_0.3.2         pkgconfig_2.0.3        farver_2.1.1          
 [65] sass_0.4.5             utf8_1.2.3             ggplotify_0.1.0        tidyselect_1.2.0       rlang_1.0.6            reshape2_1.4.4         munsell_0.5.0          tools_4.2.2           
 [73] cachem_1.0.6           downloader_0.4         cli_3.6.0              gsubfn_0.7             generics_0.1.3         RSQLite_2.2.20         gson_0.0.9             evaluate_0.20         
 [81] stringr_1.5.0          fastmap_1.1.0          yaml_2.3.7             ggtree_3.6.2           knitr_1.42             bit64_4.0.5            tidygraph_1.2.3        caTools_1.18.2        
 [89] purrr_1.0.1            KEGGREST_1.38.0        ggraph_2.1.0           nlme_3.1-160           aplot_0.1.9            compiler_4.2.2         png_0.1-8              treeio_1.22.0         
 [97] tibble_3.1.8           tweenr_2.0.2           bslib_0.4.2            stringi_1.7.12         lattice_0.20-45        Matrix_1.5-1           vctrs_0.5.2            pillar_1.8.1          
[105] lifecycle_1.0.3        jquerylib_0.1.4        GlobalOptions_0.1.2    data.table_1.14.6      cowplot_1.1.1          bitops_1.0-7           patchwork_1.1.2        qvalue_2.30.0         
[113] R6_2.5.1               KernSmooth_2.23-20     gridExtra_2.3          codetools_0.2-18       MASS_7.3-58.1          gtools_3.9.4           chron_2.3-59           proto_1.0.0           
[121] rjson_0.2.21           withr_2.5.0            GenomeInfoDbData_1.2.9 parallel_4.2.2         ggfun_0.0.9            tidyr_1.3.0            HDO.db_0.99.1          rmarkdown_2.20        
[129] ggforce_0.4.1

ADD REPLY • link 21 months ago Rodrigo ▴ 10

0

Entering edit mode

Hi Rodrigo,

Please follow the vignette example. Does the map function work for you? If so, it is something with the input. You can provide the smallest reproducible error-causing input and I can see why that happens.

If it doesn't work. Please provide the arguments with which you initiate the stirngdb object, basically this line:

string_db <- STRINGdb$new( version="11.5", species=9606, score_threshold=200, input_directory="")

Best, Damian.

ADD REPLY • link 21 months ago damian.szk ▴ 110

1

Entering edit mode

Hi Damian,

Thanks a lot. As it happens, I'm stupid and used an unexistent name column :) I got a bit misled because of the warning message.

ADD REPLY • link 21 months ago Rodrigo ▴ 10