Newer
Older
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
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!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="Ruqian Lyu" />
<title>Crossover-identification-with-sscocaller-and-comapr</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/journal.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/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/navigation-1.1/codefolding.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>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<link rel="icon" href="https://github.com/workflowr/workflowr-assets/raw/master/img/reproducible.png">
<!-- Add a small amount of space between sections. -->
<style type="text/css">
div.section {
padding-top: 12px;
}
</style>
<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
{ }
@media screen {
code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
.sourceCode .row {
width: 100%;
}
.sourceCode {
overflow-x: auto;
}
.code-folding-btn {
margin-right: -30px;
}
</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>
<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: 51px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 56px;
margin-top: -56px;
}
.section h2 {
padding-top: 56px;
margin-top: -56px;
}
.section h3 {
padding-top: 56px;
margin-top: -56px;
}
.section h4 {
padding-top: 56px;
margin-top: -56px;
}
.section h5 {
padding-top: 56px;
margin-top: -56px;
}
.section h6 {
padding-top: 56px;
margin-top: -56px;
}
.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 -->
<style type="text/css">
.code-folding-btn { margin-bottom: 4px; }
</style>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
}
.tocify .list-group-item {
border-radius: 0px;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<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">REJY_2020_Spermtyping</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="about.html">About</a>
</li>
<li>
<a href="license.html">License</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://gitlab.svi.edu.au/rlyu/rejy_2020_single-sperm-co-calling">
<span class="fa fa-github"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div class="btn-group pull-right">
<button type="button" class="btn btn-default btn-xs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu" style="min-width: 50px;">
<li><a id="rmd-show-all-code" href="#">Show All Code</a></li>
<li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>
</ul>
</div>
<h1 class="title toc-ignore">Crossover-identification-with-sscocaller-and-comapr</h1>
<h4 class="author">Ruqian Lyu</h4>
</div>
<p>
<button type="button" class="btn btn-default btn-workflowr btn-workflowr-report" data-toggle="collapse" data-target="#workflowr-report">
<span class="glyphicon glyphicon-list" aria-hidden="true"></span> workflowr <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span>
</button>
</p>
<div id="workflowr-report" class="collapse">
<ul class="nav nav-tabs">
<li class="active">
<a data-toggle="tab" href="#summary">Summary</a>
</li>
<li>
<a data-toggle="tab" href="#checks"> Checks <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> </a>
</li>
<li>
<a data-toggle="tab" href="#versions">Past versions</a>
</li>
</ul>
<div class="tab-content">
<div id="summary" class="tab-pane fade in active">
<p>
<strong>Last updated:</strong> 2021-05-14
</p>
<p>
<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 6 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 1
</p>
<p>
<strong>Knit directory:</strong> <code>~/Projects/rejy_2020_single-sperm-co-calling/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
</p>
<p>
This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a
href="https://github.com/jdblischak/workflowr">workflowr</a> (version 1.6.2). The <em>Checks</em> tab describes the reproducibility checks that were applied when the results were created. The <em>Past versions</em> tab lists the development history.
</p>
<hr>
</div>
<div id="checks" class="tab-pane fade">
<div id="workflowr-checks" class="panel-group">
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguncommittedchanges"> <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> <strong>R Markdown file:</strong> uncommitted changes </a>
</p>
</div>
<div id="strongRMarkdownfilestronguncommittedchanges" class="panel-collapse collapse">
<div class="panel-body">
<p>The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run <code>wflow_publish</code> to commit the R Markdown file and build the HTML.</p>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongEnvironmentstrongempty"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Environment:</strong> empty </a>
</p>
</div>
<div id="strongEnvironmentstrongempty" class="panel-collapse collapse">
<div class="panel-body">
<p>Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.</p>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongSeedstrongcodesetseed20190102code"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Seed:</strong> <code>set.seed(20190102)</code> </a>
</p>
</div>
<div id="strongSeedstrongcodesetseed20190102code" class="panel-collapse collapse">
<div class="panel-body">
<p>The command <code>set.seed(20190102)</code> was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.</p>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongSessioninformationstrongrecorded"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Session information:</strong> recorded </a>
</p>
</div>
<div id="strongSessioninformationstrongrecorded" class="panel-collapse collapse">
<div class="panel-body">
<p>Great job! Recording the operating system, R version, and package versions is critical for reproducibility.</p>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongCachestrongnone"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Cache:</strong> none </a>
</p>
</div>
<div id="strongCachestrongnone" class="panel-collapse collapse">
<div class="panel-body">
<p>Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.</p>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongFilepathsstrongrelative"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>File paths:</strong> relative </a>
</p>
</div>
<div id="strongFilepathsstrongrelative" class="panel-collapse collapse">
<div class="panel-body">
<p>Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.</p>
</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaurlyurejy2020singlespermcocallingtree264a63473afba209c49e430667cb16d008a22998targetblank264a634a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/rlyu/rejy_2020_single-sperm-co-calling/tree/264a63473afba209c49e430667cb16d008a22998" target="_blank">264a634</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaurlyurejy2020singlespermcocallingtree264a63473afba209c49e430667cb16d008a22998targetblank264a634a" class="panel-collapse collapse">
<div class="panel-body">
<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/rlyu/rejy_2020_single-sperm-co-calling/tree/264a63473afba209c49e430667cb16d008a22998" target="_blank">264a634</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
</p>
<pre><code>
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Untracked files:
Untracked: .DS_Store
Untracked: .Renviron
Untracked: .gitignore
Untracked: .snakemake/
Untracked: CTAGAGTCACCCAAAT-1/
Untracked: _workflowr.yml
Untracked: analysis/2020-11-17_REJY_forming-RangedSummarizedExperiment.Rmd
Untracked: analysis/2021-03-03_diagnostic-functions-comapr.Rmd
Untracked: analysis/BatchComparison-scCNV-2021-04-30.Rmd
Untracked: analysis/Crossover-identification-with-sscocaller-and-comapr.Rmd
Untracked: analysis/_site.yml
Untracked: analysis/figure/
Untracked: analysis/rejy.bib
Untracked: analysis/subsampled-wc522-crossovers_2021-05-04.Rmd
Untracked: code/checkChr15results.R
Untracked: code/compareCO.R
Untracked: code/knownCrossovers.R
Untracked: code/openBam
Untracked: code/openBam.nim
Untracked: code/plot_count.R
Untracked: code/possorted_bam.bam
Untracked: code/sscocaller
Untracked: code/sscocallerMulti
Untracked: code/testFileStream
Untracked: code/testFileStream.nim
Untracked: code/testLocalTp
Untracked: code/testLocalTp.nim
Untracked: code/testOpenVCF
Untracked: code/testOpenVCF.nim
Untracked: data/
Untracked: multi.log
Untracked: output/19_altCount.mtx
Untracked: output/19_header.mtx
Untracked: output/19_snpAnnot.txt
Untracked: output/19_totalCount.mtx
Untracked: output/19_vi.mtx
Untracked: output/19_viSegInO.txt
Untracked: output/AA-6_altCount.mtx
Untracked: output/AA-6_header.mtx
Untracked: output/AA-6_snpAnnot.txt
Untracked: output/AA-6_totalCount.mtx
Untracked: output/AA-6_vi.mtx
Untracked: output/AA-6_viSegInO.txt
Untracked: output/WC_522/
Untracked: output/WC_526/
Untracked: output/analysisRDS/
Untracked: output/chr15_altCount.mtx
Untracked: output/chr15_header.mtx
Untracked: output/chr15_snpAnnot.txt
Untracked: output/chr15_totalCount.mtx
Untracked: output/chr15_vi.mtx.gz
Untracked: output/chr15_viSegInO.txt
Untracked: output/chr19_altCount.mtx
Untracked: output/chr19_header.mtx
Untracked: output/chr19_snpAnnot.txt
Untracked: output/chr19_totalCount.mtx
Untracked: output/chr19_vi.mtx
Untracked: output/chr19_viSegInO.txt
Untracked: output/figures/
Untracked: output/firstBatch/
Untracked: output/new-chr15_altCount.mtx
Untracked: output/new-chr15_header.mtx
Untracked: output/new-chr15_snpAnnot.txt
Untracked: output/new-chr15_totalCount.mtx
Untracked: output/new-chr15_vi.mtx
Untracked: output/new-chr15_viSegInO.txt
Untracked: output/nohup.out
Untracked: output/outputR/
Untracked: output/secondBatch/
Untracked: output/test-chr15_altCount.mtx
Untracked: output/test-chr15_header.mtx
Untracked: output/test-chr15_snpAnnot.txt
Untracked: output/test-chr15_totalCount.mtx
Untracked: output/test-chr15_vi.mtx
Untracked: output/test-chr15_viSegInO.txt
Untracked: percell.wc522.af.corange.chr1.pdf
Untracked: percell.wc522.af.corange.chr10.pdf
Untracked: percell.wc522.af.corange.chr11.pdf
Untracked: percell.wc522.af.corange.chr12.pdf
Untracked: percell.wc522.af.corange.chr13.pdf
Untracked: percell.wc522.af.corange.chr14.pdf
Untracked: percell.wc522.af.corange.chr15.pdf
Untracked: percell.wc522.af.corange.chr16.pdf
Untracked: percell.wc522.af.corange.chr17.pdf
Untracked: percell.wc522.af.corange.chr18.pdf
Untracked: percell.wc522.af.corange.chr19.pdf
Untracked: percell.wc522.af.corange.chr2.pdf
Untracked: percell.wc522.af.corange.chr3.pdf
Untracked: percell.wc522.af.corange.chr4.pdf
Untracked: percell.wc522.af.corange.chr5.pdf
Untracked: percell.wc522.af.corange.chr6.pdf
Untracked: percell.wc522.af.corange.chr7.pdf
Untracked: percell.wc522.af.corange.chr8.pdf
Untracked: percell.wc522.af.corange.chr9.pdf
Untracked: percell.wc522.af.corange.pdf
Untracked: percell/
Untracked: references/
Untracked: rejy_2020_single-sperm-co-calling.Rproj
Untracked: runCompareCO.out
Untracked: runScaNBC.out
Untracked: runSscal.out
Untracked: run_compareCO.snk
Untracked: run_scalBc.snk
Untracked: run_scalability.snk
Untracked: run_sscocaller.snk
Untracked: run_sscocallerSec.snk
Untracked: runsSclog.out
Untracked: runsscocaller.log.out
Untracked: runssscocallerSec.out
Untracked: runssscocallersub.out
Untracked: runsubedWC522.out
Untracked: single.log
Untracked: slurm-86395.out
Untracked: slurm-86396.out
Untracked: slurm-86397.out
Untracked: slurm-86398.out
Untracked: slurm-86399.out
Untracked: slurm-86400.out
Untracked: slurm-86401.out
Untracked: slurm-86402.out
Untracked: slurm-86403.out
Untracked: slurm-86404.out
Untracked: slurm-86405.out
Untracked: slurm-86406.out
Untracked: slurm-86407.out
Untracked: slurm-86408.out
Untracked: slurm-86409.out
Untracked: slurm-86410.out
Untracked: slurm-86411.out
Untracked: slurm-86412.out
Untracked: slurm-86413.out
Untracked: slurm-86414.out
Untracked: slurm-86415.out
Untracked: slurm-86416.out
Untracked: slurm-86418.out
Untracked: slurm-86419.out
Untracked: slurm-86420.out
Untracked: slurm-86421.out
Untracked: slurm-86422.out
Untracked: slurm-86423.out
Untracked: slurm-86424.out
Untracked: slurm-86425.out
Untracked: slurm-86426.out
Untracked: slurm-86427.out
Untracked: slurm-86428.out
Untracked: slurm-86429.out
Untracked: slurm-86430.out
Untracked: slurm-86431.out
Untracked: slurm-86432.out
Untracked: slurm-86433.out
Untracked: slurm-86434.out
Untracked: slurm-86435.out
Untracked: slurm-86436.out
Untracked: slurm-86437.out
Untracked: slurm-86438.out
Untracked: slurm-86439.out
Untracked: slurm-86440.out
Untracked: slurm-86441.out
Untracked: slurm-86442.out
Untracked: slurm-86443.out
Untracked: slurm-86444.out
Untracked: slurm-86445.out
Untracked: slurm-86446.out
Untracked: slurm-86447.out
Untracked: slurm-86448.out
Untracked: slurm-86449.out
Untracked: slurm-86450.out
Untracked: slurm-86451.out
Untracked: slurm-86452.out
Untracked: slurm-86453.out
Untracked: slurm-86454.out
Untracked: slurm-86455.out
Untracked: slurm-86456.out
Untracked: slurm-86457.out
Untracked: slurm-86458.out
Untracked: slurm-86459.out
Untracked: slurm-86460.out
Untracked: slurm-86461.out
Untracked: slurm-86462.out
Untracked: slurm-86463.out
Untracked: slurm-86464.out
Untracked: slurm-86465.out
Untracked: slurm-86466.out
Untracked: slurm-86467.out
Untracked: slurm-86468.out
Untracked: slurm-86470.out
Untracked: slurm-86471.out
Untracked: slurm-86472.out
Untracked: slurm-86473.out
Untracked: slurm-86474.out
Untracked: slurm-86475.out
Untracked: slurm-86476.out
Untracked: slurm-86477.out
Untracked: slurm-86478.out
Untracked: slurm-86479.out
Untracked: slurm-86480.out
Untracked: slurm-86482.out
Untracked: slurm-86483.out
Untracked: slurm-86484.out
Untracked: slurm-86485.out
Untracked: slurm-86486.out
Untracked: slurm-86487.out
Untracked: slurm-86488.out
Untracked: slurm-86489.out
Untracked: slurm-86490.out
Untracked: slurm-86491.out
Untracked: slurm-86492.out
Untracked: slurm-86493.out
Untracked: slurm-86494.out
Untracked: slurm-86495.out
Untracked: slurm-86496.out
Untracked: slurm-86497.out
Untracked: slurm-86498.out
Untracked: slurm-86499.out
Untracked: slurm-86500.out
Untracked: slurm-86501.out
Untracked: slurm-86502.out
Untracked: slurm-86503.out
Untracked: slurm-86504.out
Untracked: slurm-86505.out
Untracked: slurm-86506.out
Untracked: slurm-86507.out
Untracked: slurm-86508.out
Untracked: slurm-86509.out
Untracked: slurm-86510.out
Untracked: slurm-86511.out
Untracked: slurm-86512.out
Untracked: slurm-86513.out
Untracked: somefile.txt
Untracked: submit-runMulti.sh
Untracked: submit-runSNK-hmm-CNV.sh
Untracked: submit-runScal.sh
Untracked: submit-runScalnbc.sh
Untracked: submit-runSingle.sh
Untracked: submit-runcompareco.sh
Untracked: submit-runsscocaller.sh
Untracked: submit-runsscocallerSec.sh
Untracked: submit-subsample-wc522.sh
Untracked: test/
Unstaged changes:
Modified: analysis/2020-11-17_REJY_CLT-method-and-output-explanation.Rmd
Modified: analysis/2020-11-17_REJY_CLT-method-and-output-explanation.html
Deleted: analysis/Crossover-identification-example-dataset.Rmd
Modified: analysis/Individualized-genetic-map-using-sscocaller-comapr_2021-02-15.Rmd
Modified: analysis/Individualized-genetic-map-using-sscocaller-comapr_2021-04-28.Rmd
Modified: code/sscocaller.nim
Modified: code/sscocallerMulti.nim
Staged changes:
New: analysis/Crossover-identification-example-dataset.Rmd
</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
</p>
</div>
</div>
</div>
</div>
<hr>
</div>
<div id="versions" class="tab-pane fade">
<p>
There are no past versions. Publish this analysis with <code>wflow_publish()</code> to start tracking its development.
</p>
<hr>
</div>
</div>
</div>
<div id="introduction" class="section level2">
<h2>Introduction</h2>
<p>We will demonstrate the usage of <a href="https://gitlab.svi.edu.au/biocellgen-public/sscocaller"><code>sscocaller</code></a> and <a href="https://github.com/ruqianl/comapr"><code>comapr</code></a> for identifying and visualising crossovers regions from single-sperm DNA sequencing dataset.</p>
<p><code>sscocaller</code>(<a href="https://gitlab.svi.edu.au/biocellgen-public/sscocaller" class="uri">https://gitlab.svi.edu.au/biocellgen-public/sscocaller</a>) applies a binomial Hidden Markov Model for inferring haplotypes of single sperm genomes from the aligned DNA reads in a BAM file. The inferred haplotype sequence can then be used for calling crossovers by identifying haplotype shifts (see <a href="https://github.com/ruqianl/comapr"><code>comapr</code></a> ).</p>
</div>
<div id="downloading-example-dataset" class="section level2">
<h2>Downloading example dataset</h2>
<p>An individual mouse genetic map was constructed by DNA sequencing of 217 sperm cells from a F1 hybrid mouse (B6 X CAST) <span class="citation">(Hinch et al. 2019)</span>. We will apply <code>sscocaller</code> on this dataset and it can be downloaded from GEO (Gene Expression Omnibus) with accession <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE125326">GSE125326</a></p>
<p>The slurm submission script <code>submit-wgetSRAFastqdump.sh</code> at <a href="https://gitlab.svi.edu.au/biocellgen-public/hinch-single-sperm-DNA-seq-processing.git">repo</a> can be used for downloading the <code>.sra</code> files and dumping them into paired fastq files for each sperm (including two bulk sperm samples).</p>
</div>
<div id="dataset-preprocessing" class="section level2">
<h2>Dataset preprocessing</h2>
<div id="alignment" class="section level3">
<h3>1 Alignment</h3>
<p>The downloaded fastq files for each sperm cells (and the bulk sperm samples) were aligned to mouse reference genome mm10. The workflow <a href="https://gitlab.svi.edu.au/biocellgen-public/hinch-single-sperm-DNA-seq-processing.git"><code>run_alignment.snk</code></a> which is a <a href="https://snakemake.readthedocs.io/en/stable/">Snakemake</a> file that defined steps/rules including</p>
<ul>
<li>running <a href="https://github.com/OpenGene/fastp"><code>fastp</code></a> for filtering reads and adapter trimming</li>
<li>running <a href="https://github.com/lh3/minimap2"><code>minimap2</code></a> for mapping reads to reference genome mm10</li>
<li>running GATK MarkDuplicates</li>
<li>running GATK AddOrReplaceReadGroup</li>
<li>running sorting and indexing bam files using <code>samtools</code></li>
</ul>
</div>
<div id="subsample-reads-and-append-cb-tag" class="section level3">
<h3>2 Subsample reads and append CB tag</h3>
<p><code>sscocaller</code> is designed to process DNA reads with CB (cell barcode) tags from all single sperm cells stored in one BAM file. And to reduce some processing burdens, the mapped reads for each sperm were de-duplicated and subsamples to a fraction of 0.5.</p>
<p>In addition, before merging reads from each sperm, the CB (cell barcode, the SRR ID) tag was appended to each DNA read using <a href="https://github.com/ruqianl/appendCB">appendCB</a>. Refer to steps defined in <code>run_subsample.snk</code>.</p>
</div>
<div id="merge-single-sperm-bam-files-into-one-bam" class="section level3">
<h3>3 Merge single-sperm bam files into one Bam</h3>
<p><code>samtools</code> was used for merge CB-taged reads from all single sperm to one BAM file. See <code>submit-mergeBams.sh</code>.</p>
</div>
<div id="finding-informative-snp-markers" class="section level3">
<h3>4 Finding informative SNP markers</h3>
<p>The informative SNP markers are those SNPs which differ between the two mouse stains that were used to generate the F1 hybrid mouse (CAST and BL6). The following steps were applied which largely align with what has been described in the original paper <span class="citation">(Hinch et al. 2019)</span>.</p>
<p>The bulk sperm sample <code>SRR8454653</code> was used for calling de no vo variants for this mouse individual using GATK HaplotypeCaller. Only the HET SNPs with <code>MQ>50</code> AND <code>DP>10</code> AND <code>DP<80</code> were kept. The SNPs were further filtered to only keep the positions which have been called as Homo_alternative <code>CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz</code> downloaded from the dbsnp database from Mouse Genome Project<span class="citation">(Keane et al. 2011)</span>.</p>
</div>
</div>
<div id="running-sscocaller" class="section level2">
<h2>Running sscocaller</h2>
<p>With the DNA reads from each sperm were tagged and merged into one BAM file, we can run <code>sscocaller</code> for inferring the haplotype states against the list of informative SNP markers for each chromosome in each sperm.</p>
<p>The required input files are:</p>
<pre><code>mergedBam = "output/alignment/mergedBam/mergedAll.bam",
vcfRef="output/variants/denovoVar/SRR8454653.mkdup.sort.rg.filter.snps.castVar.vcf.gz",
bcFile="output/alignment/mergedBam/mergedAll.bam.barcodes.txt"</code></pre>
<p><code>run_sscocaller.snk</code> defines the rule for running <code>sscocaller</code> on each chromosome for sperm cells. The command line was:</p>
<pre><code>sscocaller --threads 4 --chrom "chr1" --chrName chr {input.mergedBam} \
{input.vcfRef} {input.bcFile} --maxTotalReads 150 --maxDP 10 \
sscocaller/hinch/hinch_
</code></pre>
</div>
<div id="output-files" class="section level2">
<h2>Output files</h2>
<p>The generated output files (for each chromosome, here showing chr1):</p>
<ul>
<li>hinch_chr1_altCount.mtx, sparse matrix file, containing the alternative allele counts (the CAST alleles)</li>
<li>hinch_chr1_totalCount.mtx, sparse matrix file, containing the total allele counts (the CAST + BL6 alleles)</li>
<li>hinch_chr1_vi.mtx, sparse matrix file, containing the inferred Viterbi state (haplotype state) for each chromosome against the list of SNP markers in "_snpAnnot.txt".</li>
<li>hinch_chr1_viSegInfo.txt, txt file, containing the inferred Viterbi state segments information. Details below</li>
<li>hinch_chr1_snpAnnot.txt, txt file, containing the row annotations (SNPs) for the above sparse matrices.</li>
</ul>
<p>**Note, the columns in these sparse matrices correspond to cells in the input <code>bcFile</code>.</p>
<p>**_viSegInfo.txt** contains summary statistics of inferred Viterbi state segments.</p>
<p>A Viterbi segment is defined by a list of consecutive SNPs having the same Viterbi state.</p>
<p>The columns in the _viSegInfo.txt are:</p>
<ul>
<li>ithSperm,</li>
<li>Starting SNP position,</li>
<li>Ending SNP position,</li>
<li>the number of SNPs supporting the segment</li>
<li>the log likelihood ratio of the Viterbi segment</li>
<li>the inferred hidden state</li>
</ul>
<p><strong>log likelihood ratio </strong></p>
<p>The loglikelihood ratio is calculated by taking the inferred log likelihood and subtract the reversed log likelihood.</p>
<p>For example, the segment with two SNPs in the figure below: <img src="../public/meta_images/ratio_ll.png" /> The numbers in brackets indicating the (alternative allele counts, total allele counts) aligned to the two SNP positions.</p>
<p>The inferred log likelihood can be expressed as:</p>
<p><span class="math display">\[
inferredLogll = log(Trans_L)+log(dbinom(3,4,0.9))+log(dbinom(4,4,0.9))+log(Trans_R)
\]</span> The reversed log likelihood is then:</p>
<p><span class="math display">\[
reversedLogll = log(noTrans_L)+log(dbinom(3,4,0.1))+log(dbinom(4,4,0.1))+log(noTrans_R)
\]</span> Hence the logllRatio:</p>
<p><span class="math display">\[
logllRatio = inferredLogll - reversedLogll
\]</span></p>
<p>A larger <code>logllRatio</code> indicating we are more confident with the inferred Viterbi states for markers in the segment.</p>
</div>
<div id="diagnosic-plots" class="section level2">
<h2>Diagnosic plots</h2>
<p>The output files from <code>sscocaller</code> can be directly parsed through <code>readHapState</code> function. However, we have a look at some cell-level metrics and segment-level metrics before we parse the <code>sscocaller</code> output files.</p>
<div id="per-cell-qc" class="section level3">
<h3>Per cell QC</h3>
<p>The function <code>perCellQC</code> generates cell-level metrics in a data.frame and the plots in a list.</p>
<p>We first identify the relevant file paths:</p>
<p><code>dataset_dir</code> is the ouput directory from running <code>sscocaller</code> and <code>barcodeFile_path</code> points to the file containing the list of cell barcodes.</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">suppressPackageStartupMessages</span>({</span>
<span id="cb3-2"><a href="#cb3-2"></a> <span class="kw">library</span>(comapr)</span>