R语言获取 GO/KEGG 中某一通路的基因集 |
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有时候我们想看某一特定通路的富集情况，这时就需要获取该通路的基因集。 一、从 GO 中获取下载脚本 getGoTerm.R，获取所有的 GO geneSet，然后保存为RData，因为 get_GO_data 这一步非常耗时。 source("getGoTerm.R") GO_DATA getKEGG(c("hsa04930", "hsa04940", "hsa04950")) $`Type II diabetes mellitus` [1] "INS" "INSR" "IRS1" "IRS2" "IRS4" "PIK3R1" "PIK3R2" [8] "PIK3R3" "PIK3CA" "PIK3CD" "PIK3CB" "SLC2A4" "ADIPOQ" "MAPK1" [15] "MAPK3" "MTOR" "PRKCZ" "SOCS1" "SOCS2" "SOCS3" "SOCS4" [22] "IKBKB" "MAPK8" "MAPK10" "MAPK9" "TNF" "PRKCD" "PRKCE" [29] "PDX1" "MAFA" "SLC2A2" "HK3" "HK1" "HK2" "HKDC1" [36] "GCK" "PKM" "PKLR" "KCNJ11" "ABCC8" "CACNA1C" "CACNA1D" [43] "CACNA1A" "CACNA1B" "CACNA1E" "CACNA1G" $`Type I diabetes mellitus` [1] "INS" "GAD1" "GAD2" "PTPRN" "PTPRN2" "CPE" [7] "HSPD1" "ICA1" "HLA-DMA" "HLA-DMB" "HLA-DOA" "HLA-DOB" [13] "HLA-DPA1" "HLA-DPB1" "HLA-DQA1" "HLA-DQA2" "HLA-DQB1" "HLA-DRA" [19] "HLA-DRB1" "HLA-DRB3" "HLA-DRB4" "HLA-DRB5" "CD80" "CD86" [25] "CD28" "IL12A" "IL12B" "IL2" "IFNG" "HLA-A" [31] "HLA-B" "HLA-C" "HLA-F" "HLA-G" "HLA-E" "FASLG" [37] "FAS" "PRF1" "GZMB" "LTA" "TNF" "IL1A" [43] "IL1B" $`Maturity onset diabetes of the young` [1] "HHEX" "MNX1" "ONECUT1" "PDX1" "NR5A2" "NEUROG3" "NKX2-2" [8] "NKX6-1" "PAX6" "PAX4" "NEUROD1" "RFX6" "HES1" "HNF1B" [15] "FOXA2" "MAFA" "HNF4A" "HNF1A" "HNF4G" "FOXA3" "PKLR" [22] "SLC2A2" "INS" "IAPP" "GCK" "BHLHA15" Ref用clusterProfiler做GSEA（一） 从KEGG的pathway中提取gene symbol R-下载某一条通路的所有基因名字（KEGG） |
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