How to run protein-protein interaction on R using STRING database

Question

[tpm]

Hi,

I would like to know the codes precisely on how I load data with my list of protein targets that I want analysed on the String database. So far I know that I have to run these codes below.

From then on, I do not know how I should:

1. Load the dataset

2. Link the dataset on R in order to run it on R

   install.packages("BiocManager")
   install.packages("STRINGdb")
   library("STRINGdb")
   

PS. I am a beginner level in programming.

Thank you in advance, I hope for a favourable response.

[gcasabo]

Hi, first of all I'm not an expert at all but I've been working with STRINGdb in R this week and I wanted to contribute to the community.

Firstly, in case you don't know it, you can use the gene symbols you have in your Excel without mapping them to a STRING id, so you can save yourself the mapping part.

You don't say how (in which format) do you want the network, it can be as a PNG image or as a TSV file, for example. If you want an image you can just use the get_png method from STRINGdb package. An easy way to use it in your example would be something like this:

  string_db$get_png(p$gene, file="network.png")

However, I don't know why you put 00 as score_threshold, the medium (and by default) value is 400 and if you to set it lower than that, I suggest a value of 200.

Hope it serves. Regards

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[Ram]

How did you install STRINGdb, a Biooconductor package, using install.packages() instead of BiocManager::install()?

[tpm]

May I kindly RamRS,

From then on, what codes can I use to avoid getting the error below: Error in tempMatr[i, ] : incorrect number of dimensions

The question is on linking the dataset on R to the STRING database.

install.packages("BiocManager")
install.packages("STRINGdb")
library(BiocManager)
library("STRINGdb")
string_db <- STRINGdb$new( version="11", species=469008, score_threshold=00, input_directory="")
library(readxl)
p <- read_excel("1.xlsx")
View(p)
p_mapped <- string_db$map( p, "gene", removeUnmappedRows = TRUE )
**Error in tempMatr[i, ] : incorrect number of dimensions**

Basically the proteins I want to establish a network for are in this sharable link: https://drive.google.com/file/d/1aJisbhWyqUFcx_wIBMxcDtw5fMIE-z5d/view?usp=sharing

I would greatly appreciate the help very much.

[Hamid Ghaedi]

I am not sure why, but when you read your data from Excel into R some times you will face difficulty around your data type. Conveting your data to data frame by data.frame function resovled the issue. look at :

   str(p)
    tibble [331 x 3] (S3: tbl_df/tbl/data.frame)
     $ Protein IDs: chr [1:331] "UPI000012B727" "UPI000012A283" "UPI000013B55B" "UPI00000540BA" ...
     $ dprfH-wt   : num [1:331] 5.24 4.64 3.95 3.92 3.79 ...
     $ gene       : chr [1:331] "GLND_ECOLI" "EUTC_ECOLI" "MSCM_ECOLI" "TATA_ECOLI" ...

converting p to pp as a dataframe

pp <- data.frame(p)

str(pp)
'data.frame':   331 obs. of  3 variables:
 $ Protein.IDs: chr  "UPI000012B727" "UPI000012A283" "UPI000013B55B" "UPI00000540BA" ...
 $ dprfH.wt   : num  5.24 4.64 3.95 3.92 3.79 ...
 $ gene       : chr  "GLND_ECOLI" "EUTC_ECOLI" "MSCM_ECOLI" "TATA_ECOLI" ...

Now it works,

string_db <- STRINGdb$new( version="11", species=469008, score_threshold=00, input_directory="")
p_mapped <- string_db$map( pp, "gene", removeUnmappedRows = TRUE )
Warning:  we couldn't map to STRING 100% of your identifiers

It seems your identifires are not in correct format.

[Hamid Ghaedi]

Also, make sure you pasted correct codes for package installation. Is it possible to install a Biocondoctor package by install.packages() function?

[tpm]

Its better to check on the website on installations: anyhow if you run this code it will work,

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("STRINGdb")