-
Notifications
You must be signed in to change notification settings - Fork 50
/
background_functions.html
642 lines (568 loc) · 20 KB
/
background_functions.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
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="author" content="Brian J. Knaus" />
<meta name="date" content="2018-06-25" />
<title>Background functions</title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/sandstone.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/accessible-code-block-0.0.1/empty-anchor.js"></script>
<link href="site_libs/anchor-sections-1.0/anchor-sections.css" rel="stylesheet" />
<script src="site_libs/anchor-sections-1.0/anchor-sections.js"></script>
<!-- Global Site Tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-107144798-3"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments)};
gtag('js', new Date());
gtag('config', 'UA-107144798-3');
</script>
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css" data-origin="pandoc">
code.sourceCode > span { display: inline-block; line-height: 1.25; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode { white-space: pre; position: relative; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
code.sourceCode { white-space: pre-wrap; }
code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ background-color: #f8f8f8; }
@media screen {
code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ef2929; } /* Alert */
code span.an { color: #8f5902; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #c4a000; } /* Attribute */
code span.bn { color: #0000cf; } /* BaseN */
code span.cf { color: #204a87; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4e9a06; } /* Char */
code span.cn { color: #000000; } /* Constant */
code span.co { color: #8f5902; font-style: italic; } /* Comment */
code span.cv { color: #8f5902; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #8f5902; font-weight: bold; font-style: italic; } /* Documentation */
code span.dt { color: #204a87; } /* DataType */
code span.dv { color: #0000cf; } /* DecVal */
code span.er { color: #a40000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #0000cf; } /* Float */
code span.fu { color: #000000; } /* Function */
code span.im { } /* Import */
code span.in { color: #8f5902; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #204a87; font-weight: bold; } /* Keyword */
code span.op { color: #ce5c00; font-weight: bold; } /* Operator */
code span.ot { color: #8f5902; } /* Other */
code span.pp { color: #8f5902; font-style: italic; } /* Preprocessor */
code span.sc { color: #000000; } /* SpecialChar */
code span.ss { color: #4e9a06; } /* SpecialString */
code span.st { color: #4e9a06; } /* String */
code span.va { color: #000000; } /* Variable */
code span.vs { color: #4e9a06; } /* VerbatimString */
code span.wa { color: #8f5902; font-weight: bold; font-style: italic; } /* Warning */
</style>
<script>
// apply pandoc div.sourceCode style to pre.sourceCode instead
(function() {
var sheets = document.styleSheets;
for (var i = 0; i < sheets.length; i++) {
if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
try { var rules = sheets[i].cssRules; } catch (e) { continue; }
for (var j = 0; j < rules.length; j++) {
var rule = rules[j];
// check if there is a div.sourceCode rule
if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") continue;
var style = rule.style.cssText;
// check if color or background-color is set
if (rule.style.color === '' && rule.style.backgroundColor === '') continue;
// replace div.sourceCode by a pre.sourceCode rule
sheets[i].deleteRule(j);
sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
}
}
})();
</script>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
<link rel="stylesheet" href="styles.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 61px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 66px;
margin-top: -66px;
}
.section h2 {
padding-top: 66px;
margin-top: -66px;
}
.section h3 {
padding-top: 66px;
margin-top: -66px;
}
.section h4 {
padding-top: 66px;
margin-top: -66px;
}
.section h5 {
padding-top: 66px;
margin-top: -66px;
}
.section h6 {
padding-top: 66px;
margin-top: -66px;
}
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
</head>
<body>
<div class="container-fluid main-container">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Population genetics and genomics in R</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="TOC.html">Table of contents</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Part I
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="Introduction.html">Introduction</a>
</li>
<li>
<a href="Getting_ready_to_use_R.html">Getting ready to use R</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Part II
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="Data_Preparation.html">Data preparation</a>
</li>
<li>
<a href="First_Steps.html">First steps</a>
</li>
<li>
<a href="Population_Strata.html">Population strata and clone correction</a>
</li>
<li>
<a href="Locus_Stats.html">Locus-based statistics and missing data</a>
</li>
<li>
<a href="Genotypic_EvenRichDiv.html">Genotypic evenness, richness, and diversity</a>
</li>
<li>
<a href="Linkage_disequilibrium.html">Linkage disequilibrium</a>
</li>
<li>
<a href="Pop_Structure.html">Population structure</a>
</li>
<li>
<a href="Minimum_Spanning_Networks.html">Minimum Spanning Networks</a>
</li>
<li>
<a href="AMOVA.html">AMOVA</a>
</li>
<li>
<a href="DAPC.html">Discriminant analysis of principal components (DAPC)</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Part III
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="intro_vcf.html">Population genomics and HTS</a>
</li>
<li>
<a href="reading_vcf.html">Reading VCF data</a>
</li>
<li>
<a href="analysis_of_genome.html">Analysis of genomic data</a>
</li>
<li>
<a href="gbs_analysis.html">Analysis of GBS data</a>
</li>
<li>
<a href="clustering_plot.html">Clustering plot</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Workshops
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">ICPP</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="workshop_icpp.html">Preparation</a>
</li>
<li>
<a href="intro_vcf.html">Introduction</a>
</li>
<li>
<a href="reading_vcf.html">VCF data</a>
</li>
<li>
<a href="quality_control.html">Quality control</a>
</li>
<li>
<a href="gbs_analysis.html">Analysis of GBS data</a>
</li>
<li>
<a href="analysis_of_genome.html">Analysis of genome data</a>
</li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">APS Southern Division</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="workshop_southernAPS.html">Preparation</a>
</li>
<li>
<a href="intro_vcf.html">Introduction</a>
</li>
<li>
<a href="reading_vcf.html">VCF data</a>
</li>
<li>
<a href="quality_control.html">Quality control</a>
</li>
<li>
<a href="gbs_analysis.html">Analysis of GBS data</a>
</li>
</ul>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
About
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="Authors.html">Authors</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Appendices
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="intro_to_R.html">Introduction to R</a>
</li>
<li>
<a href="Data_sets.html">Data sets</a>
</li>
<li>
<a href="funpendix.html">Function glossary</a>
</li>
<li>
<a href="background_functions.html">Background_functions</a>
</li>
<li>
<a href="https://github.com/grunwaldlab/Population_Genetics_in_R/">Source Code</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">Background functions</h1>
<h4 class="author">Brian J. Knaus</h4>
<h4 class="date">June 25, 2018</h4>
</div>
<div id="background-functions" class="section level2">
<h2>Background functions</h2>
<p>Some R functions may be used frequently throughout analyses yet to new users some of them may appear non-intuitive. Here we attempt to identify some of these functions and illustrate their use.</p>
</div>
<div id="apply" class="section level2">
<h2>apply()</h2>
<p>One of R’s shortcomings is that <code>for()</code> loops are relatvely slow. Historically this was a greater problem and recent versions of R have improved the performance of these loops. Because of the performance cost associated with <code>for</code> loops it is generally recommended to avoid them in your R code, particularly when performance is an issue. If you have a task that requires iteration and you want performance that is greater than a <code>for()</code> loop will provide, you should consider <code>apply()</code>. We’ll create a matrix to illustrate its use.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a>tmp <-<span class="st"> </span><span class="kw">matrix</span>(<span class="kw">rep</span>(<span class="dv">1</span><span class="op">:</span><span class="dv">3</span>, <span class="dt">times =</span> <span class="dv">3</span>), <span class="dt">ncol =</span> <span class="dv">3</span>)</span>
<span id="cb1-2"><a href="#cb1-2"></a>tmp</span></code></pre></div>
<pre><code>## [,1] [,2] [,3]
## [1,] 1 1 1
## [2,] 2 2 2
## [3,] 3 3 3</code></pre>
<p>The function <code>apply()</code> will ‘apply’ a function over the rows or columns of a matrix. Here we’ll use the function <code>sum()</code> to illustrate this.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="kw">apply</span>(tmp, <span class="dt">MARGIN =</span> <span class="dv">1</span>, sum)</span></code></pre></div>
<pre><code>## [1] 3 6 9</code></pre>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw">apply</span>(tmp, <span class="dt">MARGIN =</span> <span class="dv">2</span>, sum)</span></code></pre></div>
<pre><code>## [1] 6 6 6</code></pre>
<p>The <code>MARGIN</code> parameter specifies whether to operate on rows or columns. I remember how 1 and 2 behave by remembering that when we specify the rows of a matrix with the square brackets (<code>[]</code>) we use the first position before the comma. To specify the columns we use the second position or after the comma.</p>
<p>More information on <code>apply()</code> can be found by consulting it’s manual page.</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>?apply</span></code></pre></div>
</div>
<div id="sweep" class="section level2">
<h2>sweep()</h2>
<p>The function <code>sweep()</code> is similar to <code>apply()</code> in that it iterates over the rows or columns of a matrix. However, it takes the additional parameters <code>STATS</code> and <code>FUN</code>. The parameter <code>FUN</code> is a function to be used. This may be an R function or a custom function you’ve created. The parameter <code>STATS</code> is a vector of data to be used by the function. Here we use <code>apply()</code> to create a mean for each column and then use <code>sweep()</code> to divide the values in the matrix by their column mean.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>my_means <-<span class="st"> </span><span class="kw">apply</span>(tmp, <span class="dt">MARGIN =</span> <span class="dv">2</span>, sum) <span class="op">/</span><span class="st"> </span><span class="kw">nrow</span>(tmp)</span>
<span id="cb8-2"><a href="#cb8-2"></a><span class="kw">sweep</span>(tmp, <span class="dt">MARGIN =</span> <span class="dv">2</span>, <span class="dt">STATS =</span> my_means, <span class="dt">FUN =</span> <span class="st">"/"</span>)</span></code></pre></div>
<pre><code>## [,1] [,2] [,3]
## [1,] 0.5 0.5 0.5
## [2,] 1.0 1.0 1.0
## [3,] 1.5 1.5 1.5</code></pre>
<p>More information on <code>sweep()</code> can be found by consulting it’s manual page.</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1"></a>?sweep</span></code></pre></div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
});
});
</script>
<!-- code folding -->
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>