How to download genes from MSigdb in R?

Question

[Amr]

How to download all genes inside all gene sets in C6 (oncogenic signature gene sets, 189 gene sets) in Molecular signature database (Msigdb) I want to download the all genes inside 189 gene sets in R in a data frame?

Thanks in advance

Answer 1

[rpolicastro]

With the msigdbr R library

library("msigdbr")
library("tidyverse")

df <- bind_rows(msigdbr("Homo sapiens", "C6"))

Answer 2

[Amr]

library(msigdbr)

genesets = msigdbr(species = "Homo sapiens", category = "C6",subcategory = NULL)
View(genesets)

unique_genes <- genesets%>% distinct(gene_symbol)
View(unique_genes)

[Ram]

IMO View is not a good command as it is specific to GUI applications such as RStudio. Use head() or str() as appropriate instead.

[Amr]

Thanks a lot for your comment :)

[Ram]

Please accept all answers that work for you. Asking a question, then ignoring existing answers to accept your own answer is bad etiquette. rpolicastro's answer is more to the point than yours.

[Amr]

Actually I wanted my answer :) plus I tried his answer but did not work with me, Also, I am new here and don't know that I should accept all answers, but I also accepted his answer.

[Ram]

Actually I wanted my answer

What do you mean by that?

I tried his answer but did not work with me

Please give feedback to rpolicastro so he can improve his answer/debug your code. Comparing your answers, his answer should work. Did you want just the unique gene symbols (available as a column in the df data.frame in his answer?

I am new here and don't know that I should accept all answers

No problem, you're encouraged to accept all answers that are given to you in a timely fashion if they work for you. On the other hand, ignoring a timely answer (especially one that gets you > 80% of the way) and then adding your own is not good etiquette. Please don't think that you need to accept all answers - you should ideally give feedback to good responses and even feel free to ignore useless responses, but not engaging with someone that put effort into your problem is a little rude.

[Amr]

I mean that I wanted to extract the unique genes by firstly, putting all genes inside all genes sets same as I asked. I implemented this :

dfox <- msigdbr("Homo sapiens", "C6") |>
+   map(as_tibble_col, column_name="gene") |>
+   bind_rows(.id="geneset_name")
Error in map(msigdbr("Homo sapiens", "C6"), as_tibble_col, column_name = "gene") : 
  could not find function "map"

I don't know if got confused and saw it in another website or it's changed plus I also don't know what is the advantages that someone gets if I vote for his/her answer that's why I didn't voted for it, and when I clicked on right mark I did that because I thought that this means that this answer is what I wanted to know for my question.

In addition, as someone new, I don't have the intention to ignore someone or act rude or anything like that, simply I just didn't know what should be done and what are the rules. Please don't judge people so fast :)

[rpolicastro]

I fixed the code shortly after posting, so you just had the bad luck of trying the code in that short timespan between edits.

[Ram]

I apologize for my rude comments - I've seen users ask a question, ignore answers by other people and add their own answer (often the exact same as the other person's answer) and accept their added answer.

The upvotes/points for accepted answers are minimal, that's not why you need to accept all answers that work for you; it's a matter of closure/record. You have a question that could have multiple answers. In the future, someone may have a similar question but the answer you accepted may not work for them. The approach in a different answer might. For this reason, accepting all answers that work + providing feedback to answers that don't results in a transparent log of things that work and don't work in your problem area. This benefits the community at large.

[Amr]

@Ram No problem :) Wish you a good day :)