-
Notifications
You must be signed in to change notification settings - Fork 13
/
vcfR_object.html
709 lines (627 loc) · 22.8 KB
/
vcfR_object.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
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>vcfR objects</title>
<script src="site_libs/header-attrs-2.16/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.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>
<style>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;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<!-- Global Site Tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-107144798-2"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments)};
gtag('js', new Date());
gtag('config', 'UA-107144798-2');
</script>
<!-- Global Site Tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-107144798-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments)};
gtag('js', new Date());
gtag('config', 'UA-107144798-1');
</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>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<link rel="stylesheet" href="styles.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
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;
}
details > summary > p:only-child {
display: inline;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.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: #adb5bd;
}
.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 type="text/javascript">
// 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 the anchor link active (and if it's in a dropdown, also mark that active)
var dropdown = menuAnchor.closest('li.dropdown');
if (window.bootstrap) { // Bootstrap 4+
menuAnchor.addClass('active');
dropdown.find('> .dropdown-toggle').addClass('active');
} else { // Bootstrap 3
menuAnchor.parent().addClass('active');
dropdown.addClass('active');
}
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
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-bs-toggle="collapse" data-target="#navbar" data-bs-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">vcfR</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="rlanguage.html">R language</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Tutorial
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="quick_intro.html">A quick introduction</a>
</li>
<li>
<a href="vcf_data.html">VCF data</a>
</li>
<li>
<a href="vcfR_object.html">vcfR objects</a>
</li>
<li>
<a href="how_much_memory.html">How much memory</a>
</li>
<li>
<a href="matrices.html">Extracting matrices</a>
</li>
<li>
<a href="tidy_vcfR.html">Tidy vcfR</a>
</li>
<li>
<a href="chromR_object.html">chromR objects</a>
</li>
<li>
<a href="visualization_1.html">Visualization 1</a>
</li>
<li>
<a href="visualization_2.html">Visualization 2</a>
</li>
<li>
<a href="sequence_coverage.html">Sequence coverage</a>
</li>
<li>
<a href="filtering_data.html">Filtering data</a>
</li>
<li>
<a href="ranking_data.html">Ranking data</a>
</li>
<li>
<a href="windowing.html">Windowing</a>
</li>
<li>
<a href="genetic_differentiation.html">Genetic differentiation</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
GBS class
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="gbs_class.html">GBS class</a>
</li>
<li>
<a href="vcf_data.html">VCF data</a>
</li>
<li>
<a href="extract_data.html">Extract data</a>
</li>
<li>
<a href="depth_plot.html">Depth plot</a>
</li>
<li>
<a href="missing_data.html">Missing data</a>
</li>
<li>
<a href="censoring_data.html">Censoring data</a>
</li>
<li>
<a href="omitting_data.html">Omitting data</a>
</li>
<li>
<a href="apply.html">Apply</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Ploidy
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="ploidy.html">Ploidy</a>
</li>
<li>
<a href="determining_ploidy_1.html">Determining ploidy 1</a>
</li>
<li>
<a href="determining_ploidy_2.html">Determining ploidy 2</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Export
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="export.html">Overview</a>
</li>
<li>
<a href="export_vcfgz.html">Export to *vcf.gz</a>
</li>
<li>
<a href="export_genind_genclone.html">Genind and Genclone</a>
</li>
<li>
<a href="export_genlight_snpclone.html">Genlight and SNPclone</a>
</li>
<li>
<a href="dnabin.html">DNAbin</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
FAQ
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="subset_data_to_1chrom.html">Subset to 1 chromosome</a>
</li>
<li>
<a href="missing_data.html">Missing data</a>
</li>
<li>
<a href="vcf_software.html">VCF software</a>
</li>
<li>
<a href="dip_to_hap.html">Haploidizing diploid data</a>
</li>
<li>
<a href="compiling_vcfR.html">Compiling vcfR</a>
</li>
<li>
<a href="reporting_issue.html">Reporting an issue</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<p>
<center>
<h3>vcfR documentation</h3>
by
<br>
Brian J. Knaus and Niklaus J. Grünwald
</center>
</p>
<div id="header">
<h1 class="title toc-ignore">vcfR objects</h1>
</div>
<div id="TOC">
<ul>
<li><a href="#creation" id="toc-creation">Creation</a></li>
<li><a href="#summarization"
id="toc-summarization">Summarization</a></li>
<li><a href="#queries" id="toc-queries">Queries</a></li>
<li><a href="#subsetting" id="toc-subsetting">Subsetting</a></li>
</ul>
</div>
<p>The package vcfR uses two objects to contain data: vcfR and chromR.
The chromR object will be covered in a later section. The vcfR object is
intended to contain data read in from a variant call format (VCF) file.
Once stored in this object the data may be manipulated in a number of
ways. It may also be used as part of the more complicated chromR object.
Here we provide an overview of the vcfR object.</p>
<div id="creation" class="section level2">
<h2>Creation</h2>
<p>A first step in understanding the vcfR object is to create one so we
can explore it.</p>
<pre class="r"><code>library(vcfR)
vcf_file <- system.file("extdata", "pinf_sc50.vcf.gz", package = "pinfsc50")
vcf <- read.vcfR( vcf_file, verbose = FALSE )</code></pre>
<p>Here we start by loading the library vcfR to make its functions
available to us. The function <code>system.file()</code> locates teh
file ‘pinf_sc50.vcf.gz’ in the R package ‘pinfsc50.’ This library may be
in different locations on different system, so this function helps us
find our example file. In practice, you’ll substitute this step by using
the name of your data file and any relevant path information (if the
file is not in your working directory). The function
<code>read.vcfR()</code> reads in a VCF file and returns a vcfR object.
Here we’ve called this vcfR object ‘vcf.’ We’ve also set ‘verbose =
FALSE’ in order to improve the formating of this page. In practice, tou
will typically leave ‘verbose = TRUE’ (it’s default) so that progress is
reported. Large files may require some patience to import, so progress
provides important feedback during this step.</p>
</div>
<div id="summarization" class="section level2">
<h2>Summarization</h2>
<p>Once we’re imorted our VCF data, we’ll want to explore our vcfR
object to validate that its contents are what we expect. Two relevant
tools are the object’s <code>show</code> method as wellas the
<code>head()</code> command.</p>
<pre class="r"><code>vcf</code></pre>
<pre><code>## ***** Object of Class vcfR *****
## 18 samples
## 1 CHROMs
## 22,031 variants
## Object size: 22.4 Mb
## 7.929 percent missing data
## ***** ***** *****</code></pre>
<p>When we execute the object’s name with no function we implement the
object’s <code>show</code> method. The <code>show</code> method for vcfR
objects reports a summary of the object’s contents. Here we see that we
have 18 samples and 22,031 variants. We should know how many samples
were in our experiment. This number should be compared to the value
reported here. We may similarly have some information about how many
variants should be in the file. That number can also be compared to the
value reported here.</p>
<pre class="r"><code>head(vcf)</code></pre>
<pre><code>## [1] "***** Object of class 'vcfR' *****"
## [1] "***** Meta section *****"
## [1] "##fileformat=VCFv4.1"
## [1] "##source=\"GATK haplotype Caller, phased with beagle4\""
## [1] "##FILTER=<ID=LowQual,Description=\"Low quality\">"
## [1] "##FORMAT=<ID=AD,Number=.,Type=Integer,Description=\"Allelic depths fo [Truncated]"
## [1] "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read [Truncated]"
## [1] "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">"
## [1] "First 6 rows."
## [1]
## [1] "***** Fixed section *****"
## CHROM POS ID REF ALT QUAL FILTER
## [1,] "Supercontig_1.50" "41" NA "AT" "A" "4784.43" NA
## [2,] "Supercontig_1.50" "136" NA "A" "C" "550.27" NA
## [3,] "Supercontig_1.50" "254" NA "T" "G" "774.44" NA
## [4,] "Supercontig_1.50" "275" NA "A" "G" "714.53" NA
## [5,] "Supercontig_1.50" "386" NA "T" "G" "876.55" NA
## [6,] "Supercontig_1.50" "462" NA "T" "G" "1301.07" NA
## [1]
## [1] "***** Genotype section *****"
## FORMAT BL2009P4_us23 DDR7602
## [1,] "GT:AD:DP:GQ:PL" "1|1:0,7:7:21:283,21,0" "1|1:0,6:6:18:243,18,0"
## [2,] "GT:AD:DP:GQ:PL" "0|0:12,0:12:36:0,36,427" "0|0:20,0:20:60:0,60,819"
## [3,] "GT:AD:DP:GQ:PL" "0|0:27,0:27:81:0,81,1117" "0|0:26,0:26:78:0,78,1077"
## [4,] "GT:AD:DP:GQ:PL" "0|0:29,0:29:87:0,87,1243" "0|0:27,0:27:81:0,81,1158"
## [5,] "GT:AD:DP:GQ:PL" "0|0:26,0:26:78:0,78,1034" "0|0:30,0:30:90:0,90,1242"
## [6,] "GT:AD:DP:GQ:PL" "0|0:23,0:23:69:0,69,958" "0|0:36,0:36:99:0,108,1556"
## IN2009T1_us22 LBUS5
## [1,] "1|1:0,8:8:24:324,24,0" "1|1:0,6:6:18:243,18,0"
## [2,] "0|0:16,0:16:48:0,48,650" "0|0:20,0:20:60:0,60,819"
## [3,] "0|0:23,0:23:69:0,69,946" "0|0:26,0:26:78:0,78,1077"
## [4,] "0|0:32,0:32:96:0,96,1299" "0|0:27,0:27:81:0,81,1158"
## [5,] "0|0:41,0:41:99:0,122,1613" "0|0:30,0:30:90:0,90,1242"
## [6,] "0|0:35,0:35:99:0,105,1467" "0|0:36,0:36:99:0,108,1556"
## NL07434
## [1,] "1|1:0,12:12:36:486,36,0"
## [2,] "0|0:28,0:28:84:0,84,948"
## [3,] "0|1:19,20:39:99:565,0,559"
## [4,] "0|1:19,19:38:99:523,0,535"
## [5,] "0|1:22,22:44:99:593,0,651"
## [6,] "0|1:29,25:54:99:723,0,876"
## [1] "First 6 columns only."
## [1]
## [1] "Unique GT formats:"
## [1] "GT:AD:DP:GQ:PL"
## [1]</code></pre>
<p>The <code>head()</code> function reports the head, or the top, of an
object. A vcfR object consists of three slots: meta, fix and gt. Here we
see the first few lines or rows of each slot. More information on VCF
data can be found in the section <a
href="./vcf_data.html">vcf_data</a>.</p>
</div>
<div id="queries" class="section level2">
<h2>Queries</h2>
<p>Once we have validated that our vcfR object contains the data we
expect we may want to explore it further.</p>
<pre class="r"><code>head(is.polymorphic(vcf, na.omit = TRUE))</code></pre>
<pre><code>## Supercontig_1.50_41 Supercontig_1.50_136 Supercontig_1.50_254
## FALSE TRUE TRUE
## Supercontig_1.50_275 Supercontig_1.50_386 Supercontig_1.50_462
## TRUE TRUE TRUE</code></pre>
<pre class="r"><code>head(is.biallelic(vcf))</code></pre>
<pre><code>## [1] TRUE TRUE TRUE TRUE TRUE TRUE</code></pre>
<p>VCF files report only variable, or polymorphic, positions. This means
that all positions in your VCF file should have been polymorphic. The
package vcfR allows you to manipulate VCF data. For example, you may
want to omit certain samples. If the samples you omit were the only ones
polymorphic for certain positions you may have rendered these positions
unpolymorphic. Note that columns of the ‘fix’ slot contains summaries
over all samples. If you remove samples then these summaries are no
longer accurate, so make sure you keep this in mind when making these
changes. This function allows you to query the positions to validate
that they are polymorphic.</p>
<p>The function <code>is.biallelic()</code> queries positions to
determine if they contain no more than two alleles. Some downstream
analyses can only handle biallelic loci. Some R object from other
packages, or file formats for other softwares, can only handle biallelic
loci. This funciton helps validate if loci contain more than two alleles
and can help manage this situation if desired.</p>
<pre class="r"><code>vcf2 <- extract.indels(vcf)</code></pre>
<p>Variants contained in VCF data may include single nucleotide
polymorphisms (SNPs) as well as indels or more complicated features.
Some analyses may require that only SNPs are used (e.g., when a mutation
model is used). In these cases it may be useful to subset the data to
only the SNPs. The function <code>extract.indels()</code> may be used
for this. Note that it is different from the previous queries in that it
subsets the vcfR object for you instead of just returning an index. This
allows the rapid creation of vcfR object that should only contain
SNPs.</p>
</div>
<div id="subsetting" class="section level2">
<h2>Subsetting</h2>
<p>The package vcfR provides the ability to manipulte VCF data. With
this functionality comes the ability to create invalide VCF files. When
done with forethought this provides valuable options. When not done with
forethought this is likely to create problems. Please familiarize
yourself with the VCF specification if your goal is to output valid VCF
files. If your goal is to create different formats of your data then
these tools may be helpful.</p>
<pre class="r"><code>vcf[,1:4]</code></pre>
<pre><code>## ***** Object of Class vcfR *****
## 3 samples
## 1 CHROMs
## 22,031 variants
## Object size: 11.9 Mb
## 2.875 percent missing data
## ***** ***** *****</code></pre>
<pre class="r"><code>vcf[1:4,]</code></pre>
<pre><code>## ***** Object of Class vcfR *****
## 18 samples
## 1 CHROMs
## 4 variants
## Object size: 0 Mb
## 6.944 percent missing data
## ***** ***** *****</code></pre>
<pre class="r"><code>vcf[is.biallelic(vcf),]</code></pre>
<pre><code>## ***** Object of Class vcfR *****
## 18 samples
## 1 CHROMs
## 21,719 variants
## Object size: 21.8 Mb
## 7.991 percent missing data
## ***** ***** *****</code></pre>
<p>The square brackets (<code>[]</code>) have been implemented for vcfR
objects in order to allow their manipulation appear similar to other R
objects. The vcfR object’s ‘fix’ and ‘gt’ slots consist of matrices.
When columns are selected, by subsetting after the comma, only columns
from the ‘gt’ slot are manipulated and the ‘fix’ slot is maintained.
Note that the first column of the ‘gt’ slot contains the format
information for all of the subsequent columns. This means you will
typically want to include the first column. When selecting rows, by
indexing before the comma, both the ‘fix’ and ‘gt’ slots are subset.
Subsetting can be performed in typical R manners such as the numeric
sequences provided above. They can also be combined with the query
functions presented above to facilitate more complex operations.</p>
</div>
<center>
<hr class="style1">
<p>Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.</p>
<p>USDA Agricultural Research Service, Horticultural Crops Research Lab.</p>
</center>
</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>