Entering edit mode
4.1 years ago
evelyn
▴
230
Hello,
I have got a list of differentially expressed genes (res`) using salmon, tximport and DESeq2. Now, to interpret better, I want to add annotation for these genes based on gene models. But the species annotation is not already available. I tried using:
res_data <- as.data.frame(res)
gen_anotation<-gene_models.gff
left_join(res_data,gen_anotation, by ="gen")
But I got an error:
Error in UseMethod("tbl_vars") :
no applicable method for 'tbl_vars' applied to an object of class "character"
Can someone help to fix this? Thank you!
Please shoe some content of
gen_anotation
and how you loaded this into R, as it is unclear what this even is. Probably a class incompatibility towards tibbles.Here are a few lines from
gen_anotation
:I loaded this gff file directly into R. I could not find a reference on how to do it. Thank you!
How do you think R knows what to join with what? You have no "gen" column in the gff.
I was trying to find a method for that but could not find. How can I add the column. Thank you!
Is there a resource which can explain how to prepare gff file, upload and join using dplyr. Thank you
Sorry, but this is a really really bad time for one to be at the hand-holding stage of learning bioinformatics. You are going to have to learn for yourself how to google the utter basics.
I would load the GFF into R with
import
from the rtracklayer package. This will give you a nice tabular output. Then please check themerge
command on how to merge your results with the GFF.