In the Stringdb website it is possible to select the active interaction sources in settings. Among these options, let's say I am only interested in Experiments and Databases. There I can uncheck the options I don't want. I wonder if this option is available also for R STRINGdb package. The function string_db$get_interactions(exampleproteins)
returns a series of columns with the score that each option (Textmining, Experiments...) contributes with, but I can't find how to filter the score by column as in the website. Maybe an option in STRINGdb$new()
may give me the desired result? I know about the threshold I can set, but it is not what I mean. Thanks in advance for your help.
Hi, I would like to know the codes I should run to import an excel sheet with my list of protein targets that I want analysed on the String database using R. 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.