-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathTIAnnotation.html
459 lines (352 loc) · 25.4 KB
/
TIAnnotation.html
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
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
<!DOCTYPE html>
<!-- saved from url=(0014)about:internet -->
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<title>Annotation and Gene Ontology analysis of differential expression</title>
<style type="text/css">
body, td {
font-family: sans-serif;
background-color: white;
font-size: 12px;
margin: 8px;
}
tt, code, pre {
font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace;
}
h1 {
font-size:2.2em;
}
h2 {
font-size:1.8em;
}
h3 {
font-size:1.4em;
}
h4 {
font-size:1.0em;
}
h5 {
font-size:0.9em;
}
h6 {
font-size:0.8em;
}
a:visited {
color: rgb(50%, 0%, 50%);
}
pre {
margin-top: 0;
max-width: 95%;
border: 1px solid #ccc;
white-space: pre-wrap;
}
pre code {
display: block; padding: 0.5em;
}
code.r, code.cpp {
background-color: #F8F8F8;
}
table, td, th {
border: none;
}
blockquote {
color:#666666;
margin:0;
padding-left: 1em;
border-left: 0.5em #EEE solid;
}
hr {
height: 0px;
border-bottom: none;
border-top-width: thin;
border-top-style: dotted;
border-top-color: #999999;
}
@media print {
* {
background: transparent !important;
color: black !important;
filter:none !important;
-ms-filter: none !important;
}
body {
font-size:12pt;
max-width:100%;
}
a, a:visited {
text-decoration: underline;
}
hr {
visibility: hidden;
page-break-before: always;
}
pre, blockquote {
padding-right: 1em;
page-break-inside: avoid;
}
tr, img {
page-break-inside: avoid;
}
img {
max-width: 100% !important;
}
@page :left {
margin: 15mm 20mm 15mm 10mm;
}
@page :right {
margin: 15mm 10mm 15mm 20mm;
}
p, h2, h3 {
orphans: 3; widows: 3;
}
h2, h3 {
page-break-after: avoid;
}
}
</style>
<!-- Styles for R syntax highlighter -->
<style type="text/css">
pre .operator,
pre .paren {
color: rgb(104, 118, 135)
}
pre .literal {
color: rgb(88, 72, 246)
}
pre .number {
color: rgb(0, 0, 205);
}
pre .comment {
color: rgb(76, 136, 107);
}
pre .keyword {
color: rgb(0, 0, 255);
}
pre .identifier {
color: rgb(0, 0, 0);
}
pre .string {
color: rgb(3, 106, 7);
}
</style>
<!-- R syntax highlighter -->
<script type="text/javascript">
var hljs=new function(){function m(p){return p.replace(/&/gm,"&").replace(/</gm,"<")}function f(r,q,p){return RegExp(q,"m"+(r.cI?"i":"")+(p?"g":""))}function b(r){for(var p=0;p<r.childNodes.length;p++){var q=r.childNodes[p];if(q.nodeName=="CODE"){return q}if(!(q.nodeType==3&&q.nodeValue.match(/\s+/))){break}}}function h(t,s){var p="";for(var r=0;r<t.childNodes.length;r++){if(t.childNodes[r].nodeType==3){var q=t.childNodes[r].nodeValue;if(s){q=q.replace(/\n/g,"")}p+=q}else{if(t.childNodes[r].nodeName=="BR"){p+="\n"}else{p+=h(t.childNodes[r])}}}if(/MSIE [678]/.test(navigator.userAgent)){p=p.replace(/\r/g,"\n")}return p}function a(s){var r=s.className.split(/\s+/);r=r.concat(s.parentNode.className.split(/\s+/));for(var q=0;q<r.length;q++){var p=r[q].replace(/^language-/,"");if(e[p]){return p}}}function c(q){var p=[];(function(s,t){for(var r=0;r<s.childNodes.length;r++){if(s.childNodes[r].nodeType==3){t+=s.childNodes[r].nodeValue.length}else{if(s.childNodes[r].nodeName=="BR"){t+=1}else{if(s.childNodes[r].nodeType==1){p.push({event:"start",offset:t,node:s.childNodes[r]});t=arguments.callee(s.childNodes[r],t);p.push({event:"stop",offset:t,node:s.childNodes[r]})}}}}return t})(q,0);return p}function k(y,w,x){var q=0;var z="";var s=[];function u(){if(y.length&&w.length){if(y[0].offset!=w[0].offset){return(y[0].offset<w[0].offset)?y:w}else{return w[0].event=="start"?y:w}}else{return y.length?y:w}}function t(D){var A="<"+D.nodeName.toLowerCase();for(var B=0;B<D.attributes.length;B++){var C=D.attributes[B];A+=" "+C.nodeName.toLowerCase();if(C.value!==undefined&&C.value!==false&&C.value!==null){A+='="'+m(C.value)+'"'}}return A+">"}while(y.length||w.length){var v=u().splice(0,1)[0];z+=m(x.substr(q,v.offset-q));q=v.offset;if(v.event=="start"){z+=t(v.node);s.push(v.node)}else{if(v.event=="stop"){var p,r=s.length;do{r--;p=s[r];z+=("</"+p.nodeName.toLowerCase()+">")}while(p!=v.node);s.splice(r,1);while(r<s.length){z+=t(s[r]);r++}}}}return z+m(x.substr(q))}function j(){function q(x,y,v){if(x.compiled){return}var u;var s=[];if(x.k){x.lR=f(y,x.l||hljs.IR,true);for(var w in x.k){if(!x.k.hasOwnProperty(w)){continue}if(x.k[w] instanceof Object){u=x.k[w]}else{u=x.k;w="keyword"}for(var r in u){if(!u.hasOwnProperty(r)){continue}x.k[r]=[w,u[r]];s.push(r)}}}if(!v){if(x.bWK){x.b="\\b("+s.join("|")+")\\s"}x.bR=f(y,x.b?x.b:"\\B|\\b");if(!x.e&&!x.eW){x.e="\\B|\\b"}if(x.e){x.eR=f(y,x.e)}}if(x.i){x.iR=f(y,x.i)}if(x.r===undefined){x.r=1}if(!x.c){x.c=[]}x.compiled=true;for(var t=0;t<x.c.length;t++){if(x.c[t]=="self"){x.c[t]=x}q(x.c[t],y,false)}if(x.starts){q(x.starts,y,false)}}for(var p in e){if(!e.hasOwnProperty(p)){continue}q(e[p].dM,e[p],true)}}function d(B,C){if(!j.called){j();j.called=true}function q(r,M){for(var L=0;L<M.c.length;L++){if((M.c[L].bR.exec(r)||[null])[0]==r){return M.c[L]}}}function v(L,r){if(D[L].e&&D[L].eR.test(r)){return 1}if(D[L].eW){var M=v(L-1,r);return M?M+1:0}return 0}function w(r,L){return L.i&&L.iR.test(r)}function K(N,O){var M=[];for(var L=0;L<N.c.length;L++){M.push(N.c[L].b)}var r=D.length-1;do{if(D[r].e){M.push(D[r].e)}r--}while(D[r+1].eW);if(N.i){M.push(N.i)}return f(O,M.join("|"),true)}function p(M,L){var N=D[D.length-1];if(!N.t){N.t=K(N,E)}N.t.lastIndex=L;var r=N.t.exec(M);return r?[M.substr(L,r.index-L),r[0],false]:[M.substr(L),"",true]}function z(N,r){var L=E.cI?r[0].toLowerCase():r[0];var M=N.k[L];if(M&&M instanceof Array){return M}return false}function F(L,P){L=m(L);if(!P.k){return L}var r="";var O=0;P.lR.lastIndex=0;var M=P.lR.exec(L);while(M){r+=L.substr(O,M.index-O);var N=z(P,M);if(N){x+=N[1];r+='<span class="'+N[0]+'">'+M[0]+"</span>"}else{r+=M[0]}O=P.lR.lastIndex;M=P.lR.exec(L)}return r+L.substr(O,L.length-O)}function J(L,M){if(M.sL&&e[M.sL]){var r=d(M.sL,L);x+=r.keyword_count;return r.value}else{return F(L,M)}}function I(M,r){var L=M.cN?'<span class="'+M.cN+'">':"";if(M.rB){y+=L;M.buffer=""}else{if(M.eB){y+=m(r)+L;M.buffer=""}else{y+=L;M.buffer=r}}D.push(M);A+=M.r}function G(N,M,Q){var R=D[D.length-1];if(Q){y+=J(R.buffer+N,R);return false}var P=q(M,R);if(P){y+=J(R.buffer+N,R);I(P,M);return P.rB}var L=v(D.length-1,M);if(L){var O=R.cN?"</span>":"";if(R.rE){y+=J(R.buffer+N,R)+O}else{if(R.eE){y+=J(R.buffer+N,R)+O+m(M)}else{y+=J(R.buffer+N+M,R)+O}}while(L>1){O=D[D.length-2].cN?"</span>":"";y+=O;L--;D.length--}var r=D[D.length-1];D.length--;D[D.length-1].buffer="";if(r.starts){I(r.starts,"")}return R.rE}if(w(M,R)){throw"Illegal"}}var E=e[B];var D=[E.dM];var A=0;var x=0;var y="";try{var s,u=0;E.dM.buffer="";do{s=p(C,u);var t=G(s[0],s[1],s[2]);u+=s[0].length;if(!t){u+=s[1].length}}while(!s[2]);if(D.length>1){throw"Illegal"}return{r:A,keyword_count:x,value:y}}catch(H){if(H=="Illegal"){return{r:0,keyword_count:0,value:m(C)}}else{throw H}}}function g(t){var p={keyword_count:0,r:0,value:m(t)};var r=p;for(var q in e){if(!e.hasOwnProperty(q)){continue}var s=d(q,t);s.language=q;if(s.keyword_count+s.r>r.keyword_count+r.r){r=s}if(s.keyword_count+s.r>p.keyword_count+p.r){r=p;p=s}}if(r.language){p.second_best=r}return p}function i(r,q,p){if(q){r=r.replace(/^((<[^>]+>|\t)+)/gm,function(t,w,v,u){return w.replace(/\t/g,q)})}if(p){r=r.replace(/\n/g,"<br>")}return r}function n(t,w,r){var x=h(t,r);var v=a(t);var y,s;if(v){y=d(v,x)}else{return}var q=c(t);if(q.length){s=document.createElement("pre");s.innerHTML=y.value;y.value=k(q,c(s),x)}y.value=i(y.value,w,r);var u=t.className;if(!u.match("(\\s|^)(language-)?"+v+"(\\s|$)")){u=u?(u+" "+v):v}if(/MSIE [678]/.test(navigator.userAgent)&&t.tagName=="CODE"&&t.parentNode.tagName=="PRE"){s=t.parentNode;var p=document.createElement("div");p.innerHTML="<pre><code>"+y.value+"</code></pre>";t=p.firstChild.firstChild;p.firstChild.cN=s.cN;s.parentNode.replaceChild(p.firstChild,s)}else{t.innerHTML=y.value}t.className=u;t.result={language:v,kw:y.keyword_count,re:y.r};if(y.second_best){t.second_best={language:y.second_best.language,kw:y.second_best.keyword_count,re:y.second_best.r}}}function o(){if(o.called){return}o.called=true;var r=document.getElementsByTagName("pre");for(var p=0;p<r.length;p++){var q=b(r[p]);if(q){n(q,hljs.tabReplace)}}}function l(){if(window.addEventListener){window.addEventListener("DOMContentLoaded",o,false);window.addEventListener("load",o,false)}else{if(window.attachEvent){window.attachEvent("onload",o)}else{window.onload=o}}}var e={};this.LANGUAGES=e;this.highlight=d;this.highlightAuto=g;this.fixMarkup=i;this.highlightBlock=n;this.initHighlighting=o;this.initHighlightingOnLoad=l;this.IR="[a-zA-Z][a-zA-Z0-9_]*";this.UIR="[a-zA-Z_][a-zA-Z0-9_]*";this.NR="\\b\\d+(\\.\\d+)?";this.CNR="\\b(0[xX][a-fA-F0-9]+|(\\d+(\\.\\d*)?|\\.\\d+)([eE][-+]?\\d+)?)";this.BNR="\\b(0b[01]+)";this.RSR="!|!=|!==|%|%=|&|&&|&=|\\*|\\*=|\\+|\\+=|,|\\.|-|-=|/|/=|:|;|<|<<|<<=|<=|=|==|===|>|>=|>>|>>=|>>>|>>>=|\\?|\\[|\\{|\\(|\\^|\\^=|\\||\\|=|\\|\\||~";this.ER="(?![\\s\\S])";this.BE={b:"\\\\.",r:0};this.ASM={cN:"string",b:"'",e:"'",i:"\\n",c:[this.BE],r:0};this.QSM={cN:"string",b:'"',e:'"',i:"\\n",c:[this.BE],r:0};this.CLCM={cN:"comment",b:"//",e:"$"};this.CBLCLM={cN:"comment",b:"/\\*",e:"\\*/"};this.HCM={cN:"comment",b:"#",e:"$"};this.NM={cN:"number",b:this.NR,r:0};this.CNM={cN:"number",b:this.CNR,r:0};this.BNM={cN:"number",b:this.BNR,r:0};this.inherit=function(r,s){var p={};for(var q in r){p[q]=r[q]}if(s){for(var q in s){p[q]=s[q]}}return p}}();hljs.LANGUAGES.cpp=function(){var a={keyword:{"false":1,"int":1,"float":1,"while":1,"private":1,"char":1,"catch":1,"export":1,virtual:1,operator:2,sizeof:2,dynamic_cast:2,typedef:2,const_cast:2,"const":1,struct:1,"for":1,static_cast:2,union:1,namespace:1,unsigned:1,"long":1,"throw":1,"volatile":2,"static":1,"protected":1,bool:1,template:1,mutable:1,"if":1,"public":1,friend:2,"do":1,"return":1,"goto":1,auto:1,"void":2,"enum":1,"else":1,"break":1,"new":1,extern:1,using:1,"true":1,"class":1,asm:1,"case":1,typeid:1,"short":1,reinterpret_cast:2,"default":1,"double":1,register:1,explicit:1,signed:1,typename:1,"try":1,"this":1,"switch":1,"continue":1,wchar_t:1,inline:1,"delete":1,alignof:1,char16_t:1,char32_t:1,constexpr:1,decltype:1,noexcept:1,nullptr:1,static_assert:1,thread_local:1,restrict:1,_Bool:1,complex:1},built_in:{std:1,string:1,cin:1,cout:1,cerr:1,clog:1,stringstream:1,istringstream:1,ostringstream:1,auto_ptr:1,deque:1,list:1,queue:1,stack:1,vector:1,map:1,set:1,bitset:1,multiset:1,multimap:1,unordered_set:1,unordered_map:1,unordered_multiset:1,unordered_multimap:1,array:1,shared_ptr:1}};return{dM:{k:a,i:"</",c:[hljs.CLCM,hljs.CBLCLM,hljs.QSM,{cN:"string",b:"'\\\\?.",e:"'",i:"."},{cN:"number",b:"\\b(\\d+(\\.\\d*)?|\\.\\d+)(u|U|l|L|ul|UL|f|F)"},hljs.CNM,{cN:"preprocessor",b:"#",e:"$"},{cN:"stl_container",b:"\\b(deque|list|queue|stack|vector|map|set|bitset|multiset|multimap|unordered_map|unordered_set|unordered_multiset|unordered_multimap|array)\\s*<",e:">",k:a,r:10,c:["self"]}]}}}();hljs.LANGUAGES.r={dM:{c:[hljs.HCM,{cN:"number",b:"\\b0[xX][0-9a-fA-F]+[Li]?\\b",e:hljs.IMMEDIATE_RE,r:0},{cN:"number",b:"\\b\\d+(?:[eE][+\\-]?\\d*)?L\\b",e:hljs.IMMEDIATE_RE,r:0},{cN:"number",b:"\\b\\d+\\.(?!\\d)(?:i\\b)?",e:hljs.IMMEDIATE_RE,r:1},{cN:"number",b:"\\b\\d+(?:\\.\\d*)?(?:[eE][+\\-]?\\d*)?i?\\b",e:hljs.IMMEDIATE_RE,r:0},{cN:"number",b:"\\.\\d+(?:[eE][+\\-]?\\d*)?i?\\b",e:hljs.IMMEDIATE_RE,r:1},{cN:"keyword",b:"(?:tryCatch|library|setGeneric|setGroupGeneric)\\b",e:hljs.IMMEDIATE_RE,r:10},{cN:"keyword",b:"\\.\\.\\.",e:hljs.IMMEDIATE_RE,r:10},{cN:"keyword",b:"\\.\\.\\d+(?![\\w.])",e:hljs.IMMEDIATE_RE,r:10},{cN:"keyword",b:"\\b(?:function)",e:hljs.IMMEDIATE_RE,r:2},{cN:"keyword",b:"(?:if|in|break|next|repeat|else|for|return|switch|while|try|stop|warning|require|attach|detach|source|setMethod|setClass)\\b",e:hljs.IMMEDIATE_RE,r:1},{cN:"literal",b:"(?:NA|NA_integer_|NA_real_|NA_character_|NA_complex_)\\b",e:hljs.IMMEDIATE_RE,r:10},{cN:"literal",b:"(?:NULL|TRUE|FALSE|T|F|Inf|NaN)\\b",e:hljs.IMMEDIATE_RE,r:1},{cN:"identifier",b:"[a-zA-Z.][a-zA-Z0-9._]*\\b",e:hljs.IMMEDIATE_RE,r:0},{cN:"operator",b:"<\\-(?!\\s*\\d)",e:hljs.IMMEDIATE_RE,r:2},{cN:"operator",b:"\\->|<\\-",e:hljs.IMMEDIATE_RE,r:1},{cN:"operator",b:"%%|~",e:hljs.IMMEDIATE_RE},{cN:"operator",b:">=|<=|==|!=|\\|\\||&&|=|\\+|\\-|\\*|/|\\^|>|<|!|&|\\||\\$|:",e:hljs.IMMEDIATE_RE,r:0},{cN:"operator",b:"%",e:"%",i:"\\n",r:1},{cN:"identifier",b:"`",e:"`",r:0},{cN:"string",b:'"',e:'"',c:[hljs.BE],r:0},{cN:"string",b:"'",e:"'",c:[hljs.BE],r:0},{cN:"paren",b:"[[({\\])}]",e:hljs.IMMEDIATE_RE,r:0}]}};
hljs.initHighlightingOnLoad();
</script>
</head>
<body>
<h1>Annotation and Gene Ontology analysis of differential expression</h1>
<pre><code>## Loading required package: proto
</code></pre>
<pre><code>## Loading required package: grid
</code></pre>
<pre><code>## Loading required package: reshape
</code></pre>
<pre><code>## Loading required package: plyr
</code></pre>
<pre><code>## Attaching package: 'reshape'
</code></pre>
<pre><code>## The following object(s) are masked from 'package:plyr':
##
## rename, round_any
</code></pre>
<pre><code>## Loading required package: limma
</code></pre>
<p>Having found genes that are differentially expressed we would like to know what these genes are, and if they share any common functions.</p>
<p>Use iget to download the files “TomatoGO.tsv”, “TomatoGOSlim.tsv”, “ITAG2.3_HRD.tsv”, and “eval.go.R” from the ti-2013 directory to /mydata</p>
<p>Now load them into R</p>
<pre><code class="r">HRD <- read.delim("/mydata/ITAG2.3_HRD.tsv")
GO <- read.delim("/mydata/TomatoGO.tsv")
GOSlim <- read.delim("/mydata/TomatoGOSlim.tsv")
source("/mydata/eval.go.R")
</code></pre>
<ul>
<li>The HRD file contains a “human readable description” of each gene. </li>
<li>The GO files contains a numeric key for the Gene Ontology terms associated with each gene (see <a href="http://www.geneontology.org/">http://www.geneontology.org/</a> for more info).<br/></li>
<li>There are two versions of the GO files. The GOSlim file contains a subset of more general GO terms.</li>
<li>eval.go is a helper script that I wrote to automate the GO analysis</li>
</ul>
<pre><code class="r">head(HRD)
</code></pre>
<pre><code>## ITAG
## 1 Solyc00g005000.2.1
## 2 Solyc00g005020.1.1
## 3 Solyc00g005040.2.1
## 4 Solyc00g005050.2.1
## 5 Solyc00g005060.1.1
## 6 Solyc00g005070.1.1
## Description.HRD.
## 1 Aspartic proteinase nepenthesin I (AHRD V1 **-- A9ZMF9_NEPAL); contains Interpro domain(s) IPR001461 Peptidase A1
## 2 Unknown Protein (AHRD V1)
## 3 Potassium channel (AHRD V1 ***- D0EM91_9ROSI); contains Interpro domain(s) IPR000595 Cyclic nucleotide-binding
## 4 Arabinogalactan protein (AHRD V1 ***- B6SST2_MAIZE)
## 5 Unknown Protein (AHRD V1)
## 6 Unknown Protein (AHRD V1)
</code></pre>
<pre><code class="r">head(GO)
</code></pre>
<pre><code>## ITAG
## 1 Solyc00g005000.2.1
## 2 Solyc00g005040.2.1
## 3 Solyc00g005050.2.1
## 4 Solyc00g005080.1.1
## 5 Solyc00g005130.1.1
## 6 Solyc00g005150.1.1
## GO
## 1 0006508,0004190
## 2 0005774,0009611,0006635,0003988,0010118,0009507,0005777,0005730,0030551,0042802,0009644,0009695,0005242,0010111,0055085,0006813,0009789,0009860,0007623,0005739,0006550,0006552,0006574,0006699,0018874,0042967,0008076
## 3 0005829,0005739,0005886
## 4 0005524,0009570,0017111,0009575
## 5 0006508,0008234
## 6 0003676
</code></pre>
<pre><code class="r">head(GOSlim)
</code></pre>
<pre><code>## ITAG
## 1 Solyc00g005000.2.1
## 2 Solyc00g005040.2.1
## 3 Solyc00g005050.2.1
## 4 Solyc00g005080.1.1
## 5 Solyc00g005130.1.1
## 6 Solyc00g005150.1.1
## GO
## 1 0019538, 0009056, 0016787
## 2 0016020, 0005773, 0009605, 0006950, 0009056, 0009987, 0006629, 0016740, 0009536, 0005777, 0005730, 0000166, 0005515, 0009628, 0009058, 0005215, 0016043, 0006810, 0009719, 0007165, 0009856, 0009653, 0030154, 0016049, 0007275, 0008150, 0005739, 0006519, 0008152, 0005886
## 3 0005829, 0005739, 0005886
## 4 0000166, 0009536, 0016787
## 5 0019538, 0009056, 0016787
## 6 0003676
</code></pre>
<p>We can merge the descriptions with top tags results as follows:</p>
<pre><code class="r">results.temp.lyc.hrd <- merge(topTags(lrt.temp.lyc)$table, HRD, by.x = "row.names",
by.y = "ITAG", all.x = T, all.y = F, sort = F)
head(results.temp.lyc.hrd)
</code></pre>
<pre><code>## Row.names logConc logFC LR P.Value adj.P.Val
## 1 Solyc05g007950.2.1 -9.357 6.620e+00 497.6 3.088e-110 5.753e-106
## 2 Solyc02g014860.2.1 -10.000 5.960e+00 346.5 2.414e-77 2.248e-73
## 3 Solyc02g082920.2.1 -7.974 5.728e+00 320.4 1.185e-71 7.356e-68
## 4 Solyc01g005300.2.1 -9.780 5.135e+00 311.2 1.175e-69 5.473e-66
## 5 Solyc10g009150.2.1 -9.653 -1.443e+08 308.9 3.708e-69 1.364e-65
## 6 Solyc06g006000.2.1 -10.546 1.023e+01 308.6 4.392e-69 1.364e-65
## Description.HRD.
## 1 Ribonuclease T2 (AHRD V1 ***- Q6A3R1_SOLLC); contains Interpro domain(s) IPR001568 Ribonuclease T2
## 2 Chaperone protein DnaJ (AHRD V1 *-*- D2QAE1_BIFDB); contains Interpro domain(s) IPR003095 Heat shock protein DnaJ
## 3 Endochitinase (Chitinase) (AHRD V1 **** Q43184_SOLTU); contains Interpro domain(s) IPR000726 Glycoside hydrolase, family 19, catalytic
## 4 Flavin-binding kelch domain F box protein (AHRD V1 **-* D7KVS5_ARALY); contains Interpro domain(s) IPR015915 Kelch-type beta propeller
## 5 Organ-specific protein S2 (AHRD V1 ***- OSS2_PEA)
## 6 Unknown Protein (AHRD V1)
</code></pre>
<p>This shows us the descriptions of the genes most DE by temperature in lyc.</p>
<h4>Exercise 1</h4>
<p>What is the description of the gene most differentially expressed among species?</p>
<h4>Exercise 2</h4>
<p>Are the top 10 genes DE in response to cold similar or different in the 3 species?</p>
<p>Next we will analyze GO categories. First we need to install a missing package:</p>
<pre><code class="r">source("http://bioconductor.org/biocLite.R")
biocLite("geneLenDataBase")
# Answer 'y' to any questions and ignore the warning 'installed directory
# not writable...' This only needs to be done once on your machine
</code></pre>
<p>Next we need the length of each gene </p>
<pre><code class="r">library(Biostrings)
</code></pre>
<pre><code>## Loading required package: IRanges
</code></pre>
<pre><code>## Attaching package: 'IRanges'
</code></pre>
<pre><code>## The following object(s) are masked from 'package:plyr':
##
## compact, desc
</code></pre>
<pre><code>## The following object(s) are masked from 'package:base':
##
## cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin,
## pmin.int, rbind, rep.int, setdiff, table, union
</code></pre>
<pre><code class="r">itagSeqs <- read.DNAStringSet("/mydata/ITAG2.3_cdna_SHORTNAMES.fasta") #read the fasta file with the genes
itagLength <- nchar(itagSeqs) #length of each ITAG
names(itagLength) <- names(itagSeqs) #add the names
head(itagLength) #check it
</code></pre>
<pre><code>## Solyc00g005000.2.1 Solyc00g005020.1.1 Solyc00g005040.2.1
## 1693 486 392
## Solyc00g005050.2.1 Solyc00g005060.1.1 Solyc00g005070.1.1
## 983 273 81
</code></pre>
<p>Finally we can look for over-representation of GO categories
Then calling eval.go:</p>
<ul>
<li>the first argument is an object containing the results from a call to glmLRT</li>
<li>the second argument is an object with the gene lengths</li>
<li>the third argument is an object with the GO terms</li>
<li>the fourth argument is the differential expression cutoff that you want to use</li>
</ul>
<pre><code class="r">require(goseq)
</code></pre>
<pre><code>## Loading required package: goseq
</code></pre>
<pre><code>## Loading required package: BiasedUrn
</code></pre>
<pre><code>## Loading required package: geneLenDataBase
</code></pre>
<pre><code class="r">require(GO.db)
</code></pre>
<pre><code>## Loading required package: GO.db
</code></pre>
<pre><code>## Loading required package: AnnotationDbi
</code></pre>
<pre><code>## Loading required package: Biobase
</code></pre>
<pre><code>## Welcome to Bioconductor
##
## Vignettes contain introductory material. To view, type
## 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and
## for packages 'citation("pkgname")'.
</code></pre>
<pre><code>## Attaching package: 'Biobase'
</code></pre>
<pre><code>## The following object(s) are masked from 'package:Biostrings':
##
## updateObject
</code></pre>
<pre><code>## The following object(s) are masked from 'package:IRanges':
##
## updateObject
</code></pre>
<pre><code>## Loading required package: DBI
</code></pre>
<pre><code>## ```
```r
require(edgeR)
</code></pre>
<pre><code class="r">eval.go(lrt = lrt.species, ilength = itagLength, go.terms = GO, p.thresh = 0.01)
</code></pre>
<pre><code>## Using manually entered categories.
</code></pre>
<pre><code>## Calculating the p-values...
</code></pre>
<pre><code>## $de
## [1] category over_represented_pvalue
## [3] under_represented_pvalue description
## [5] ontology over.pval.adjust
## <0 rows> (or 0-length row.names)
</code></pre>
<pre><code class="r">eval.go(lrt = lrt.species, ilength = itagLength, go.terms = GOSlim, p.thresh = 0.01)
</code></pre>
<pre><code>## Using manually entered categories.
</code></pre>
<pre><code>## Calculating the p-values...
</code></pre>
<pre><code>## $de
## [1] category over_represented_pvalue
## [3] under_represented_pvalue description
## [5] ontology over.pval.adjust
## <0 rows> (or 0-length row.names)
</code></pre>
<h4>Exercise 3</h4>
<p>What GO and GOSlim categories are signficantly over-represented in genes DE by temperature?</p>
</body>
</html>