Mercurial > repos > kpbioteam > clusterprofiler_go

annotate clusterProfiler_go.R @ 4:3d18046320ce draft

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planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
author kpbioteam
date Sun, 15 Jul 2018 10:47:56 -0400
parents 7a6ba13c9381
children a12bbeb898a4
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5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff changeset
1 require("clusterProfiler", quietly = TRUE)
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49ae9762eb96 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
kpbioteam
parents: 0
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2 require("DO.db", quietly = TRUE)
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5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
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3 require("org.Hs.eg.db", quietly = TRUE)
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff changeset
4 require("ggplot2", quietly = TRUE)
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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49ae9762eb96 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
kpbioteam
parents: 0
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5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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7 args <- commandArgs(trailingOnly = TRUE)
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
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5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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9 input1 = args[1]
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
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10 output1 = args[2]
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
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11 output2 = args[3]
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
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5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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13 gene <- read.table(input1)
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49ae9762eb96 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
kpbioteam
parents: 0
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14 ego <- enrichGO(gene = c(gene$V1),
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5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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15 keyType = "ENTREZID",
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
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16 OrgDb = org.Hs.eg.db,
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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17 ont = "BP",
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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18 pAdjustMethod = "BH",
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
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19 pvalueCutoff = 0.01,
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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20 qvalueCutoff = 0.05,
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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21 readable = TRUE)
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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23 write.table(ego, output1)
5aba765e27b4 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
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24 dotplot(ego)
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3d18046320ce planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
kpbioteam
parents: 3
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25 ggsave(file = output2, device = "pdf", width = 21, height = 29, units = "cm")