Hi, I'm trying to use STRINGdb for parsing the STRING PPI network in R. However, I've run into an issue where the get_neighbors() method fails with the following error Error in as.igraph.vs(graph, v) : Invalid vertex names. It seems non of the mapped STRING_id's are included in the graph despite the network being able to be plotted.

My end goal is to be able to programmatically retrieve neighbors (and their interactions) of an arbitrary path length from specified genes.

Any insight as to how I can fix this, or if there is an alternative method I should use, would be appreciated.

library(STRINGdb)

sbd <- STRINGdb$new(
  version = "10",
  species = 9606, 
  score_threshold = 0, 
  input_directory = "A:/~~~~~~~"
  )

data(diff_exp_example1)
# example data from STRINGdb vignette 

example1_mapped <- sbd$map(diff_exp_example1, "gene", removeUnmappedRows = TRUE )

dim(example1_mapped)
# [1] 17748     4

sbd$plot_network(example1_mapped$STRING_id[1:100])
# This works, 100 vertices, 106 edges

sbd$get_neighbors(example1_mapped$STRING_id[1:100])
# Error in as.igraph.vs(graph, v) : Invalid vertex names

sgrph <- sbd$get_graph()

length(igraph::V(sgrph))
# [1] 19247

sum(example1_mapped$STRING_id %in% igraph::V(sgrph))
# [1] 0

sessionInfo()
# R version 3.5.3 (2019-03-11)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows >= 8 x64 (build 9200)
# 
# Matrix products: default
# 
# locale:
#   [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
# [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    
# 
# attached base packages:
#   [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
#   [1] STRINGdb_1.22.0
# 
# loaded via a namespace (and not attached):
#   [1] igraph_1.2.4       hash_2.2.6.1       Rcpp_1.0.1         magrittr_1.5       bit_1.1-14         blob_1.1.1        
# [7] plyr_1.8.4         caTools_1.17.1.2   tools_3.5.3        png_0.1-7          plotrix_3.7-4      KernSmooth_2.23-15
# [13] DBI_1.0.0          gtools_3.8.1       yaml_2.2.0         bit64_0.9-7        digest_0.6.18      RColorBrewer_1.1-2
# [19] bitops_1.0-6       RCurl_1.95-4.12    memoise_1.1.0      RSQLite_2.1.1      gsubfn_0.7         gdata_2.18.0      
# [25] compiler_3.5.3     gplots_3.0.1.1     chron_2.3-53       sqldf_0.4-11       proto_1.0.0        pkgconfig_2.0.2