reactomePA NO plot but I have the results excel file
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Entering edit mode
9 months ago
camillab. ▴ 40

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

RNA-Seq R reactomePA • 390 views
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