Entering edit mode
4.7 years ago
tianbian0507
•
0
I am relatively new to clusterProfiler and enrichment analysis, I tried to follow the steps from here https://yulab-smu.github.io/clusterProfiler-book/chapter3.html#msigdb-analysis to do GO, MSigDb analysis and wikiPathway on our own dataset. The gsea returned "no term enriched under specific pvalueCutoff..." for both of them. I am not sure if I did something wrong or if this is the real result which there are no enriched terms.
geneList <- global$avg_logFC
names(geneList) <- global$`rownames(Lymphoid.markers)`
geneList <- sort(geneList, decreasing = TRUE)
up.genes <- global[global$avg_logFC > 0, 1]
dn.genes <- global[global$avg_logFC < 0, 1]
up.genes <- bitr(up.genes$`rownames(Lymphoid.markers)`, fromType = "SYMBOL", toType = c("ENTREZID"), OrgDb = org.Hs.eg.db)
dn.genes <- bitr(dn.genes$`rownames(Lymphoid.markers)`, fromType = "SYMBOL", toType = c("ENTREZID"), OrgDb = org.Hs.eg.db)
msigdb <- msigdbr(species = "Homo sapiens")
#head(msigdb, 2) %>% as.data.frame
m_t2g <- msigdbr(species = "Homo sapiens", category = "H") %>%
dplyr::select(gs_id, entrez_gene)
m_t2n <- msigdbr(species = "Homo sapiens", category = "H") %>%
dplyr::select(gs_id, gs_name)
geneList2 <- geneList2[!is.na(names(geneList2))]
emsig <- enricher(up.genes[[2]], TERM2GENE=m_t2g)
emsig2 <- GSEA(geneList2, TERM2GENE = m_t2g, TERM2NAME = m_t2n)
head(summary(emsig2))
[1] ID Description setSize enrichmentScore
[5] NES pvalue p.adjust qvalues
<0 rows> (or 0-length row.names)
I used the differentially expressed gene list and separated the list into two lists based on their avg_FC values. The list is the result of Seurat.
> head(global)
# A tibble: 6 x 6
`rownames(Lymphoid.markers)` p_val avg_logFC pct.1 pct.2 p_val_adj
<chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 RPS26 3.04e-89 0.941 0.979 0.912 4.59e-85
2 APOD 6.56e-70 -1.32 0.189 0.665 9.91e-66
3 TXNIP 5.39e-57 -0.678 0.606 0.862 8.15e-53
4 HLA-C 8.96e-50 0.599 0.989 0.971 1.35e-45
5 UBC 9.03e-49 0.580 0.977 0.938 1.36e-44
6 RGCC 6.56e-48 0.875 0.767 0.509 9.91e-44
Any advice will be appreciated!
Can you do
head(up.genes[[2]])
andhead(m_t2g)
?