Hi,
I am trying to perform GO analysis with reacotmePA package and I wanted to see the GO terms for both up (log2FC>1) and down regulated genes (log2Fc<= -1). I am able to get results for the downregulated genes but not for the upregulated genes (FC >2) and I don't understand why since in my dataset I have upregulated genes and when I perform enrich pathway analysis I get a list of GO terms. where is the error? I have also removed all rows where there was NA.
my dataset:
# A tibble: 5 x 4
ENSEMBL ENTREZID log2FC FC
<chr> <dbl> <dbl> <dbl>
1 ENSG00000265991 100616231 11.5 2852.
2 ENSG00000206979 26787 11.1 2226.
3 ENSG00000229686 26793 10.7 1635.
4 ENSG00000265706 109617012 9.65 801.
5 ENSG00000202515 56662 9.51 731.
My code:
#load packages
library(org.Hs.eg.db) #human genome
library(DOSE)
library(ReactomePA) # to perform enrichment analysis
library(enrichplot) # to plot the results
library(UpSetR)
#tidy the datasets
genes <- f[[4]] #numeric vector #selected fc
names(genes) <- f[[2]] #named vector
geneLIST <- sort(genes, decreasing = T) #decreasing order
head(geneLIST)
de <- names(geneLIST)[abs(geneLIST) > 2]
x <- enrichPathway(gene=de,pvalueCutoff=0.05, readable=T)
head(as.data.frame(x))
result <- x@result
barplot(x, showCategory=10, title = " ") #plot
and I got the results but not the graph. in fact when I do head(as.data.frame(x)) I got this results but I have the excel file with the GO terms.
[1] ID Description GeneRatio BgRatio
[5] pvalue p.adjust qvalue geneID
[9] Count
<0 rows> (or 0-length row.names)
But this is the first row of the"result" file that I have exported for the upregulated genes:
ID Description GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
R-HSA-211859 R-HSA-211859 Biological oxidations 13/234 222/10654 0.001229205 0.626327002 0.626327002 MGST3/CYP26A1/CYP4F3/EPHX1/FMO1/ADH6/SLC26A2/SULT1A1/MGST1/MGST2/MARC1/ALDH3A1/ACSM2A 13
so I have GO terms
thank you very much for the help!
Camilla
Cross-posted: https://support.bioconductor.org/p/131969/