gravatar for Oli

8 hours ago by

Europe

Hello community,

I need some help to make TopGO do what i need.
I have intersected the differentially expressed genes in my RNA-seq experiment with a list of genes I'm interesed to for other reasons.
When i create the TopGO object i have some troubles with the selection function.
For the whole list of differentially expressed genes i select only those with a p-value < 0.05. What if i want to perform the enrichment analysis on the genes from the second list using the DGE from my experiment as the background?

My code is this:

background <- geneuniverse$PValue
names(background) <- geneuniverse$ensembl_gene_id
selection <- function(allScore){ return(allScore < 0.05)}
GoData <- new("topGOdata",
              ontology = "BP",
              allGenes = background,
              geneSel = selection,
              annot = annFUN.org,
              mapping = "org.Hs.eg.db", 
              ID = "ensembl",
              nodeSize = 3)

If i read my genes of interest in a vector by doing:

interesting_genes <- scan('interesting_genes.txt', header=TRUE)

How can I get TRUE/FALSE for matches between interesting genes and background?
I have already tried match, %in% and grepl, but geneSel can only be a function.
Any help?

I dont' know if it's of any help, but heres how the data look:

head(background)
ENSG00000183242 ENSG00000248347 ENSG00000172482 ENSG00000120068 ENSG00000137558 
   1.81e-15        1.15e-08        5.59e-09        5.33e-07        4.86e-06      
head(interesting_genes)
[1] "ENSG00000114779" "ENSG00000143322" "ENSG00000123130" "ENSG00000103740" "ENSG00000164398"

link

modified 7 hours ago

written
8 hours ago
by

Oli0



Source link