Hi,
I have gene ontology data that looks like this (sample data). I manually downloaded the gene ontology data from the Uniprot website.
I want to:
The output data would look like this
Please note that GO terms do not repeat in a specific cell, however, they repeat in other rows. Kindly help me to do this in R.
I did several unsuccessful trials. Hope to get help from someone. I will highly appreciate your help. Thank you so much.
Tidyverse answer
library("tidyverse")
df %>%
select(gene_id, `Gene ontology (molecular function)`) %>%
distinct %>%
group_by(`Gene ontology (molecular function)`) %>%
summarize(gene_id=str_c(gene_id, collapse=", "), `No. of Genes`=n(), .groups="drop") %>%
separate_rows(`Gene ontology (molecular function)`, sep="; ") %>%
separate(
`Gene ontology (molecular function)`, sep="\\s(?=\\[GO)",
into=c("Gene ontology (molecular function)", "Gene Ontology IDs"))
Thank you so much for this code. I tried it. It works wonderfully. Some of the GO terms are repeating (present in multiple rows_ in the output table (GO:0003735,GO:0019843). Also, can we add corresponding UniprotKBs in one more column? Thank you again.
Also, I tried exporting it as CSV. It gives out the same file. How do you export the updated dataset as CSV? Thank you again for your kind help.
You need to save the results to a variable, such as changing the first line to df2 <- df %>%, and then you can save df2 to a csv.
Thank you so much. It worked.
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df[!duplicated(df$'Gene Ontology (molecular function)'),]will work, and it will only keep the first entry of the duplicated values.See this SO post as a start:
group by GO IDs, collapse gene_id column, expand GO IDs, group by GO IDs, and count genes.