-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathRELAX.GOenrichment.Rmd
185 lines (138 loc) · 5.24 KB
/
RELAX.GOenrichment.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
---
title: "Inquiline Genomics: GO enrichment analysis of RELAX results"
output:
html_document:
toc: true
toc_float: true
toc_depth: 2
collapsed: true
number_sections: true
df_print: paged
pdf_document: default
---
<STYLE TYPE="text/css">
<!--
td{
font-family: Arial;
font-size: 8pt;
padding:0px;
cellpadding="0";
cellspacing="0"
}
th {
font-family: Arial;
font-size: 8pt;
height: 20px;
font-weight: bold;
text-align: right;
background-color: #ccccff;
}
table {
border-spacing: 0px;
border-collapse: collapse;
}
--->
</STYLE>
# R steps
```{r eval=FALSE, include=FALSE}
#source("https://bioconductor.org/biocLite.R")
#BiocInstaller::biocLite("biocUpgrade")
#BiocManager::install("GO.db")
library("topGO")
library(dplyr)
library(plyr)
library(tidyr)
```
### Read large input table
```{r}
all<-read.csv("/Users/lukas/sciebo/inquilineGenomics18/SOS/data/RELAX2.tsv",sep="\t")
```
### create topGO element for Cluster GO annotations
```{r}
scoID2go<-list()
for(i in 1:length(all$OGid)){
scoID2go[[i]]<-unlist(strsplit(as.character(all$GO[i]),", "))
names(scoID2go)[i]<-as.character(all$OGid[i])
}
```
### Prepare Objects for GO enrichment analysis
```{r}
scoNames.all<-names(scoID2go)
#restrict gene space to all SCOs orthologs
scoNames<-scoNames.all
scoNames <- factor(scoNames)
names(scoNames) <- scoNames
```
### Summarize things
```{r}
# k<0 & p<0.05
length(unlist(subset(all,p.adjust(pval,method = "fdr")<0.05 & k<1,OGid)))
# k<0 & 0.05< p <0.1
length(unlist(subset(all,p.adjust(pval,method = "fdr")<0.1 & p.adjust(pval,method = "fdr")>0.05 & k<1,OGid)))
# k<0 & p<0.05
length(unlist(subset(all,p.adjust(pval,method = "fdr")<0.05 & k>1,OGid)))
# k<0 & 0.05< p <0.1
length(unlist(subset(all,p.adjust(pval,method = "fdr")<0.1 & p.adjust(pval,method = "fdr")>0.05 & k>1,OGid)))
```
### Select Clusters of Interest from dataframe "all".
```{r}
# create a 0/1 matrix (interesting/not interesting)
######################################
## all parasites
#SCOOfInterest<-unlist(subset(all,p.adjust(P1pv,method = "fdr")<0.05 | p.adjust(AINSpv,method = "fdr")<0.05 | p.adjust(PARGpv,method = "fdr")<0.05 | p.adjust(ACHApv,method = "fdr")<0.05,OGid))
# Origin of parasitism
#SCOOfInterest<-unlist(subset(all,p.adjust(pval,method = "fdr")<0.1 & k<1,OGid))
SCOOfInterest<-unlist(subset(all,p.adjust(pval,method = "fdr")<0.1 & k>1,OGid))
#SCOOfInterest<-unlist(subset(all,p.adjust(PARGpv,method = "fdr")<0.05 ,OGid))
#SCOOfInterest<-unlist(subset(all,p.adjust(ACHApv,method = "fdr")<0.05 ,OGid))
scoList <- factor(as.integer(scoNames %in% SCOOfInterest))
table(scoList)
names(scoList) <- scoNames
relaxedSelSet<-subset(all,OGid %in% SCOOfInterest)
```
```{r}
# create object for Biological Process, Molecular Function and Cellular component:
##################################################################################
GOdata_MF <- new("topGOdata", ontology = "MF", allGenes = scoList, annot = annFUN.gene2GO, gene2GO = scoID2go)
GOdata_BP <- new("topGOdata", ontology = "BP", allGenes = scoList, annot = annFUN.gene2GO, gene2GO = scoID2go)
GOdata_CC <- new("topGOdata", ontology = "CC", allGenes = scoList, annot = annFUN.gene2GO, gene2GO = scoID2go)
# Molecular Function
####################
resultFis_MF <- runTest(GOdata_MF, algorithm = "parentchild", statistic = "fisher")
table_MF <- GenTable(GOdata_MF, parentChild = resultFis_MF, orderBy = "parentChild", ranksOf = "parentChild", topNodes = 200)
# Biological Process
####################
resultFis_BP <- runTest(GOdata_BP, algorithm = "parentchild", statistic = "fisher")
table_BP <- GenTable(GOdata_BP, parentChild = resultFis_BP, orderBy = "parentChild", ranksOf = "parentChild", topNodes = 200)
# Cellular Component
####################
resultFis_CC <- runTest(GOdata_CC, algorithm = "parentchild", statistic = "fisher")
table_CC <- GenTable(GOdata_CC, parentChild = resultFis_CC, orderBy = "parentChild", ranksOf = "parentChild", topNodes = 200)
# filter out significant GO terms:
###################################
MF <- subset(table_MF, parentChild < 0.1)
BP <- subset(table_BP, parentChild < 0.1)
CC <- subset(table_CC, parentChild < 0.1)
MF$ontology<-"MF"
BP$ontology<-"BP"
CC$ontology<-"CC"
MF
BP
CC
```
```{r}
subset(all,OGid %in% genesInTerm(GOdata_BP, "GO:0046903")[[1]] & pval<0.05)
subset(all,OGid %in% genesInTerm(GOdata_MF, "GO:0005158")[[1]] & pval<0.05)
subset(all,OGid %in% genesInTerm(GOdata_CC, "GO:0038201")[[1]] & pval<0.05)
```
### save results to file
```{r}
# Origins of social parasitism
res<-rbind(MF,BP) %>% rbind(.,CC)
#outfile<-"/Users/lukas/sciebo/inquilineGenomics18/GOenrichment/results/GOenrichment.RELAX2.parasiteOrigins.relaxedSelection.tsv"
outfile<-"/Users/lukas/sciebo/inquilineGenomics18/GOenrichment/results/GOenrichment.RELAX2.parasiteOrigins.intensifiedSelection.tsv"
write.table(res,outfile,quote=F,sep="\t",row.names = F)
cat("# GO enrichment of genes under relaxed selection (p<0.1, k<1) at any social parasite branch (at FDR<0.1), compared to Ahey, Aech, A1 and A2. \n",file=outfile)
#cat("# GO enrichment of genes under relaxed selection (p<0.05, k<1) at any social parasite branch (at FDR<0.1), compared to all other branches. \n",file=outfile)
write.table(res, outfile,append=TRUE, quote=F,sep="\t",row.names=F)
```