2 answers
With the msigdbr R library
library("msigdbr")
library("tidyverse")
df <- bind_rows(msigdbr("Homo sapiens", "C6"))
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written
by
rpolicastro
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.
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 :)
I fixed the code shortly after posting, so you just had the bad luck of trying the code in that short timespan between edits.
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.
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