Mercurial > repos > kpbioteam > clusterprofiler_go
annotate clusterProfiler_go.R @ 7:e63c8d858a65 draft default tip
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
author | kpbioteam |
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date | Mon, 16 Jul 2018 06:20:31 -0400 |
parents | 6d08a0432d3f |
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rev | line source |
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5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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1 require("clusterProfiler", quietly = TRUE) |
1
49ae9762eb96
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
kpbioteam
parents:
0
diff
changeset
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2 require("DO.db", quietly = TRUE) |
0
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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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
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4 require("ggplot2", quietly = TRUE) |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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5 |
1
49ae9762eb96
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
kpbioteam
parents:
0
diff
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6 |
0
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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7 args <- commandArgs(trailingOnly = TRUE) |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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8 |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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9 input1 = args[1] |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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10 output1 = args[2] |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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11 output2 = args[3] |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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12 |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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13 gene <- read.table(input1) |
1
49ae9762eb96
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
kpbioteam
parents:
0
diff
changeset
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14 ego <- enrichGO(gene = c(gene$V1), |
7
e63c8d858a65
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
kpbioteam
parents:
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diff
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15 keyType = "ENTREZID", |
0
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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16 OrgDb = org.Hs.eg.db, |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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17 ont = "BP", |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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18 pAdjustMethod = "BH", |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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19 pvalueCutoff = 0.01, |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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20 qvalueCutoff = 0.05, |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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21 readable = TRUE) |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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22 |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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23 write.table(ego, output1) |
5aba765e27b4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2
kpbioteam
parents:
diff
changeset
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24 dotplot(ego) |
5
a12bbeb898a4
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
kpbioteam
parents:
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diff
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25 ggsave(file = output2, device = "pdf", width = 60, height = 30, units = "cm") |