STRINGdb string_db$map error
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Entering edit mode
Jessica • 0
@9faea85b
Last seen 3 months 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 • 303 views
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Entering edit mode
damian.szk ▴ 70
@damianszk-12963
Last seen 11 hours 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.

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