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
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():
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:
Best, Damian.
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.