Non-model organism , CluserProfiler message "No gene can be mapped"
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8 weeks ago
Hi, I am using clusterProfiler to do an enrichment analysis. However, I get the warning ' No gene can be mapped.... --> Expected input gene ID: ND6,ND4,COX3,ND1,ND5,ATP6 --> return NULL...'. I am studying a non-model organism, the 'Vulpes lagopus'. My script is as follows,

mycounts<-read.csv("-B5_Counts-Arctic-fat.csv",row.names = 1)
head(mycounts)
dim(mycounts)
library(dplyr)
library(DESeq2) 
mycounts <- mycounts %>%mutate_if(is.factor, ~as.numeric(as.character(.)))
mymeta<-read.csv("-B5_mymeta.csv",stringsAsFactors = T)
mycountsGroups <- mymeta$Group
colData <- data.frame(row.names=colnames(mycounts), group_list=mycountsGroups) 
dds <- DESeqDataSetFromMatrix(countData = mycounts, colData = colData, design = ~group_list, tidy = F) 
keep <- rowSums(counts(dds)>10) >4
dds.keep <- dds[keep, ]
 dim(dds.keep)
degobj <- DESeq(dds.keep);degobj 
countdds <- counts(degobj, normalized = T) 
deg.res1 <- results(degobj, contrast=c("group_list","HFB","LFB"), lfcThreshold = 0, pAdjustMethod = 'fdr') 
dim(deg.res1)
 apply(deg.res1,2, function(x) sum(is.na(x))) 
deg.res1$padj[is.na(deg.res1$padj)] <- 1 
table(is.na(deg.res1$padj)) 
summary(deg.res1) 
library(dplyr)
 res_1<-data.frame(deg.res1)
 res_1 %>% mutate(group = case_when(log2FoldChange >0.5 & padj <= 0.05 ~ "UP",log2FoldChange <-0.5 & padj <= 0.05 ~ "DOWN",TRUE ~ "NOT_CHANGE")) -> res_2 
table(res_2$group) 
upsig <- res_2[grep(pattern = "UP",res_2[,7]),] 
downsig <- res_2[grep(pattern = "DOWN",res_2[,7]),] 
deg <- rbind(upsig,downsig)
BiocManager::install("AnnotationHub")
BiocManager::install("biomaRt")
# load package
library(AnnotationHub)
library(biomaRt)
# make a orgDb
hub <- AnnotationHub::AnnotationHub()
query(hub, "Vulpes lagopus")
Vulpes.OrgDb <- hub[["AH96456"]]
columns(Vulpes.OrgDb)
library(clusterProfiler)
df2 <- bitr(row.names(upsig), fromType = "SYMBOL",
            toType = c("ENTREZID"),
            OrgDb = Vulpes.OrgDb) 
genelist <- df2$ENTREZID
enrich.go.BP = enrichGO(gene       =genelist,
                        OrgDb = Vulpes.OrgDb,
                        keyType      = 'ENTREZID',ont= "BP",
                        pvalueCutoff = 0.05,
                        pAdjustMethod = "BH",
                        qvalueCutoff = 0.05,
                        )


--> No gene can be mapped....
--> Expected input gene ID: 23629751,23629755,23629750,23629748,23629754,23629750
--> return NULL...
ORA organism non-model • 129 views
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cross-posted on bioconductor: link

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