This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to add annotation for differentially expressed genes obtained using DESeq2

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!

rna-seq
• 2,131 views • link
written by evelyn evelyn

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.

• 0 views • link
written by ATpoint ATpoint

Here are a few lines from gen_anotation:

##gff-version 3
GV1.3ch00   maker   CDS     21882   22007   .   -   0   ID=GV006775_06g024400.1.1:cds;Parent=GV006775_06g024400.1.1;
GV1.3ch00   maker   exon    21882   22007   .   -   .   ID=GV006775_06g024400.1.1:exon:2;Parent=GV006775_06g024400.1.1;
GV1.3ch00   maker   gene    21882   22007   .   -   .   ID=GV006775_06g024400.1;Name=GV006775_06g024400.1;50S ribosomal protein;ref_id=c06g024400;
GV1.3ch00   maker   mRNA    21882   22007   126 -   .   ID=GV006775_06g024400.1.1;Parent=GV006775_06g024400.1;Name=GV006775_06g024400.1.1;50S ribosomal protein;ref_id=c06g024400;
GV1.3ch00   maker   CDS     22697   22756   .   -   0   ID=GV006775_00g008910.1.1:cds;Parent=GV006775_00g008910.1.1;
GV1.3ch00   maker   exon    22697   22756   .   -   .   ID=GV006775_00g008910.1.1:exon:4;Parent=GV006775_00g008910.1.1;
GV1.3ch00   maker   gene    22697   22848   .   -   .   ID=GV006775_00g008910.1;Name=GV006775_00g008910.1;Ubiquitin protein;ref_id=c00g008910.1;
GV1.3ch00   maker   mRNA    22697   22848   102 -   .   ID=GV006775_00g008910.1.1;Parent=GV006775_00g008910.1;Name=GV006775_00g008910.1.1; Ubiquitin protein;ref_id=c00g008910.1;
GV1.3ch00   maker   CDS     22807   22848   .   -   0   ID=GV006775_00g008910.1.1:cds;Parent=GV006775_00g008910.1.1;
GV1.3ch00   maker   exon    22807   22848   .   -   .   ID=GV006775_00g008910.1.1:exon:3;Parent=GV006775_00g008910.1.1;

I loaded this gff file directly into R. I could not find a reference on how to do it. Thank you!

• 0 views • link
written by evelyn evelyn

How do you think R knows what to join with what? You have no "gen" column in the gff.

• 0 views • link
written by swbarnes2 swbarnes2

I was trying to find a method for that but could not find. How can I add the column. Thank you!

• 0 views • link
written by evelyn evelyn

Is there a resource which can explain how to prepare gff file, upload and join using dplyr. Thank you

• 0 views • link
written by evelyn evelyn

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.

• 0 views • link
written by swbarnes2 swbarnes2

I would load the GFF into R with import from the rtracklayer package. This will give you a nice tabular output. Then please check the merge command on how to merge your results with the GFF.

• 0 views • link
written by ATpoint ATpoint

0 answers

No answers yet.

Log in to answer this question.

More posts like this