Entering edit mode
4.0 years ago
peter.berry5
▴
60
When I try to map a set of proteins using the map function in the STRINGdb package I get the following error
Error in `[.data.frame`(dfToMap, , strColsFrom[i]) : undefined columns selected
My code is as follows
```{r}
BiocManager::install("STRINGdb")
library("STRINGdb")
#remove all previous files
rm(list=ls())
#read in proteins to be mapped
Attached_DE_Proteins <- read.csv("C:/PETER PROJECT/3d. Mass Spec Processing/Results of R Analysis/DE Gene Lists/Effect of Serum/WCL Analysis/0% Attached v 5% Attached/DE Cutoff equal 1.5/DE 1-5 Attached Cells DE Gene IDs WCL Apr19 Serum Removal.csv")
#call the string database.
#note if you supply a local input directory the DB will be cached here allowing offline use.
#species = 9606 for human
#species = 10029 for CHO
string_db <- STRINGdb$new( version="11", species=9606, score_threshold=400, input_directory="")
#map my DE proteins to the String DB
Proteins <- data.frame(Attached_DE_Proteins$HGNC_Symbol)
mapped_proteins <- string_db$map(Proteins, "gene", removeUnmappedRows = TRUE)
dput(str(Proteins))
'data.frame': 1541 obs. of 1 variable:
$ Attached_DE_Proteins$HGNC_Symbol: chr "ENO1 " "ANXA1 " "TALDO1 " "LTA4H " ...
NULL
Would I be correct in thinking that the term "gene" in the map command should be the name of the column containing the info I want to map?
Thanks