代谢组学 如何查找代谢通路
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发布时间：2022-07-10 14:28
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时间：2023-10-14 07:19
use my package clusterProfiler
http://bioconctor.org/packages/devel/bioc/html/clusterProfiler.html
> require(clusterProfiler)
> data(gcSample)
> gcSample[[3]]
[1] "4905" "10383" "10953" "645958" "7280" "10381" "5869" "5985"
[9] "23197" "290" "309" "10577" "23071" "121504" "2495" "653226"
[17] "84617"
> x <- enrichKEGG(gcSample[[3]])
Warning messages:
1: 'l2e' is deprecated, use 'list2env' instead
2: 'l2e' is deprecated, use 'list2env' instead
> summary(x)
pathwayID Description GeneRatio BgRatio
05130 hsa05130 Pathogenic Escherichia coli infection 4/17 59/5504
04145 hsa04145 Phagosome 5/17 159/5504
04540 hsa04540 Gap junction 4/17 90/5504
04962 hsa04962 Vasopressin-regulated water reabsorption 2/17 44/5504
pvalue qvalue geneID Count
05130 2.554952e-05 0.005397106 10383/7280/10381/84617 4
04145 8.823916e-05 0.009219728 10383/7280/10381/5869/84617 5
04540 1.352278e-04 0.010247594 10383/7280/10381/84617 4
04962 7.871612e-03 0.376048432 4905/5869 2
