大佬怎样富集分析自定义的基因集

[wyj20031116]

library(dplyr)
library(clusterProfiler)
library(org.Hs.eg.db)
gmt <- read.gmt('../resource/h.all.v2024.1.Hs.symbols.gmt')

转换为ENSEMBL

gmt_ensembl <- gmt %>%

首先为每个基因获取Ensembl ID映射

left_join(
bitr(.$gene, fromType = "SYMBOL", toType = "ENSEMBL", OrgDb = org.Hs.eg.db),
by = c("gene" = "SYMBOL")
) %>%

移除原来的gene符号列，保留Ensembl ID

dplyr::select(term, gene = ENSEMBL) %>%

移除未能映射的基因

filter(!is.na(gene)) %>%

去重

distinct()

enrich <- enrichCluster(object = df,
OrgDb = "org.Hs.eg.db",
type = "ownSet", # c("BP", "MF", "CC", "KEGG", "ownSet")
TERM2GENE = gmt_ensembl,
organism = "hsa",
pvalueCutoff = 0.05,
topn = 5,
seed = 123)
我想要富集Hallmark通路，但是不管是Symbol还是ENSEMBL，都是'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: ENSG00000145839,ENSG00000273506,ENSG00000100075,ENSG00000112493,ENSG00000289755,ENSG00000153094
--> return NULL...
'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: ENSG00000145839,ENSG00000273506,ENSG00000100075,ENSG00000112493,ENSG00000289755,ENSG00000153094
--> return NULL...
'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: ENSG00000145839,ENSG00000273506,ENSG00000100075,ENSG00000112493,ENSG00000289755,ENSG00000153094
--> return NULL...
'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: ENSG00000145839,ENSG00000273506,ENSG00000100075,ENSG00000112493,ENSG00000289755,ENSG00000153094
--> return NULL...'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: CCND1,PTPN21,SPARCL1,ACTA1,UQCR10,PEX11A
--> return NULL...
'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: CCND1,PTPN21,SPARCL1,ACTA1,UQCR10,PEX11A
--> return NULL...
'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: CCND1,PTPN21,SPARCL1,ACTA1,UQCR10,PEX11A
--> return NULL...
'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: CCND1,PTPN21,SPARCL1,ACTA1,UQCR10,PEX11A
--> return NULL...是哪个地方设置的有问题吗，该怎样修正代码

[junjunlab]

请阅读参考文档：

[wyj20031116]

还是会报错，按照阅读文档调整输入文件了已经gmt <- read.gmt('../resource/h.all.v2024.1.Hs.symbols.gmt')

enrich <- enrichCluster(object = df,
OrgDb = "org.Hs.eg.db",
type = "ownSet", # c("BP", "MF", "CC", "KEGG", "ownSet")
organism = "hsa",
TERM2GENE = gmt,
# TERM2NAME = ,
id.trans = TRUE, # 需要基因ID转换则设为TRUE
fromType = "SYMBOL", # 如果基因是符号格式
toType = "ENTREZID", # 转换到ENTREZID
pvalueCutoff = 0.05,
topn = 5,
seed = 123)

[wyj20031116]

就是一直为NULL

[wyj20031116]

enrich <- enrichCluster(object = df,

•                     OrgDb = "org.Hs.eg.db",
  

•                     type = "ownSet",  # c("BP", "MF", "CC", "KEGG", "ownSet")
  

•                     organism = "hsa",
  

•                     TERM2GENE = gmt,
  

•                     # TERM2NAME = ,
  

•                     pvalueCutoff = 1,
  

•                     add.gene = TRUE,
  

•                     topn = 5,
  

•                     seed = 123)
  

'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: CCND1,PTPN21,SPARCL1,ACTA1,UQCR10,PEX11A
--> return NULL...
'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: CCND1,PTPN21,SPARCL1,ACTA1,UQCR10,PEX11A
--> return NULL...
'select()' returned 1:1 mapping between keys and columns
--> No gene can be mapped....
--> Expected input gene ID: CCND1,PTPN21,SPARCL1,ACTA1,UQCR10,PEX11A
--> return NULL...
Warning messages:
1: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
11.39% of input gene IDs are fail to map...
2: In clusterProfiler::bitr(tmp$gene, fromType = fromType, toType = toType, :
2% of input gene IDs are fail to map... 即便设置p为1也一样