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
\documentclass[11pt, oneside]{article}\usepackage[]{graphicx}\usepackage[]{color}
% maxwidth is the original width if it is less than linewidth
% otherwise use linewidth (to make sure the graphics do not exceed the margin)
\makeatletter
\def\maxwidth{ %
\ifdim\Gin@nat@width>\linewidth
\linewidth
\else
\Gin@nat@width
\fi
}
\makeatother
\definecolor{fgcolor}{rgb}{0.345, 0.345, 0.345}
\newcommand{\hlnum}[1]{\textcolor[rgb]{0.686,0.059,0.569}{#1}}%
\newcommand{\hlstr}[1]{\textcolor[rgb]{0.192,0.494,0.8}{#1}}%
\newcommand{\hlcom}[1]{\textcolor[rgb]{0.678,0.584,0.686}{\textit{#1}}}%
\newcommand{\hlopt}[1]{\textcolor[rgb]{0,0,0}{#1}}%
\newcommand{\hlstd}[1]{\textcolor[rgb]{0.345,0.345,0.345}{#1}}%
\newcommand{\hlkwa}[1]{\textcolor[rgb]{0.161,0.373,0.58}{\textbf{#1}}}%
\newcommand{\hlkwb}[1]{\textcolor[rgb]{0.69,0.353,0.396}{#1}}%
\newcommand{\hlkwc}[1]{\textcolor[rgb]{0.333,0.667,0.333}{#1}}%
\newcommand{\hlkwd}[1]{\textcolor[rgb]{0.737,0.353,0.396}{\textbf{#1}}}%
\let\hlipl\hlkwb
\usepackage{framed}
\makeatletter
\newenvironment{kframe}{%
\def\at@end@of@kframe{}%
\ifinner\ifhmode%
\def\at@end@of@kframe{\end{minipage}}%
\begin{minipage}{\columnwidth}%
\fi\fi%
\def\FrameCommand##1{\hskip\@totalleftmargin \hskip-\fboxsep
\colorbox{shadecolor}{##1}\hskip-\fboxsep
% There is no \\@totalrightmargin, so:
\hskip-\linewidth \hskip-\@totalleftmargin \hskip\columnwidth}%
\MakeFramed {\advance\hsize-\width
\@totalleftmargin\z@ \linewidth\hsize
\@setminipage}}%
{\par\unskip\endMakeFramed%
\at@end@of@kframe}
\makeatother
\definecolor{shadecolor}{rgb}{.97, .97, .97}
\definecolor{messagecolor}{rgb}{0, 0, 0}
\definecolor{warningcolor}{rgb}{1, 0, 1}
\definecolor{errorcolor}{rgb}{1, 0, 0}
\newenvironment{knitrout}{}{} % an empty environment to be redefined in TeX
\usepackage{alltt} % use "amsart" instead of "article" for AMSLaTeX format
%\usepackage{geometry} % See geometry.pdf to learn the layout options. There are lots.
%\geometry{letterpaper} % ... or a4paper or a5paper or ...
%\geometry{landscape} % Activate for for rotated page geometry
%\usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
%\usepackage{graphicx} % Use pdf, png, jpg, or eps with pdflatex; use eps in DVI mode
% TeX will automatically convert eps --> pdf in pdflatex
%\usepackage{amssymb}
\usepackage[utf8]{inputenc}
%\usepackage[cyr]{aeguill}
%\usepackage[francais]{babel}
%\usepackage{hyperref}
\title{Positive selection on genes interacting with SARS-Cov2, comparison of different analysis}
\author{Marie Cariou}
\date{Janvier 2021} % Activate to display a given date or no date
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\begin{document}
\maketitle
\tableofcontents
\newpage
\section{Files manipulations}
\subsection{Read Janet Young's table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{workdir}\hlkwb{<-}\hlstr{"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"}
\hlstd{tab}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
\hlstr{"data/COVID_PAMLresults_332hits_plusBatScreens_2020_Apr14.csv"}\hlstd{),}
\hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{dec}\hlstd{=}\hlstr{","}\hlstd{)}
\hlkwd{dim}\hlstd{(tab)}
\end{alltt}
\begin{verbatim}
## [1] 332 84
\end{verbatim}
\end{kframe}
\end{knitrout}
\subsection{Read DGINN Young table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{dginnY}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
\hlstr{"data/summary_primate_young.res"}\hlstd{),}
\hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
\hlkwd{dim}\hlstd{(dginnY)}
\end{alltt}
\begin{verbatim}
## [1] 1992 7
\end{verbatim}
\end{kframe}
\end{knitrout}
\subsection{Joining Young and DGINN Young table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlcom{# correct gene names (MARC1)}
\hlstd{val_remp}\hlkwb{=}\hlkwd{as.character}\hlstd{(}\hlkwd{unique}\hlstd{(dginnY}\hlopt{$}\hlstd{Gene)[(}\hlkwd{unique}\hlstd{(dginnY}\hlopt{$}\hlstd{Gene)} \hlopt{%in%}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlstd{F])}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name}\hlkwb{<-}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name)}
\hlstd{tab}\hlopt{$}\hlstd{Gene.name[}\hlnum{158}\hlstd{]}\hlkwb{<-}\hlstd{val_remp}
\hlkwd{sum}\hlstd{(}\hlkwd{unique}\hlstd{(dginnY}\hlopt{$}\hlstd{Gene)} \hlopt{%in%} \hlkwd{unique}\hlstd{(tab}\hlopt{$}\hlstd{Gene.name))}
\end{alltt}
\begin{verbatim}
## [1] 332
\end{verbatim}
\end{kframe}
\end{knitrout}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{add_col}\hlkwb{<-}\hlkwa{function}\hlstd{(}\hlkwc{method}\hlstd{=}\hlstr{"PamlM1M2"}\hlstd{)\{}
\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstd{method,}
\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"Omega"}\hlstd{,} \hlstr{"PosSel"}\hlstd{,} \hlstr{"PValue"}\hlstd{,} \hlstr{"NbSites"}\hlstd{,} \hlstr{"PSS"}\hlstd{)]}
\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{"Omega_"}\hlstd{, method),}
\hlkwd{paste0}\hlstd{(}\hlstr{"PosSel_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{"PValue_"}\hlstd{, method),}
\hlkwd{paste0}\hlstd{(}\hlstr{"NbSites_"}\hlstd{, method),} \hlkwd{paste0}\hlstd{(}\hlstr{"PSS_"}\hlstd{, method))}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
\hlkwd{return}\hlstd{(tab)}
\hlstd{\}}
\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"PamlM1M2"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"PamlM7M8"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"BppM1M2"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{add_col}\hlstd{(}\hlstr{"BppM7M8"}\hlstd{)}
\hlcom{# Manip pour la colonne BUSTED}
\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{"BUSTED"}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"Omega"}\hlstd{,} \hlstr{"PosSel"}\hlstd{,} \hlstr{"PValue"}\hlstd{)]}
\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"Omega_BUSTED"}\hlstd{,} \hlstr{"PosSel_BUSTED"}\hlstd{,} \hlstr{"PValue_BUSTED"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
\hlstd{tmp}\hlkwb{<-}\hlstd{dginnY[dginnY}\hlopt{$}\hlstd{Method}\hlopt{==}\hlstr{"MEME"}\hlstd{,}\hlkwd{c}\hlstd{(}\hlstr{"Gene"}\hlstd{,} \hlstr{"NbSites"}\hlstd{,} \hlstr{"PSS"}\hlstd{)]}
\hlkwd{names}\hlstd{(tmp)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"Gene.name"}\hlstd{,} \hlstr{"NbSites_MEME"}\hlstd{,} \hlstr{"PSS_MEME"}\hlstd{)}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab, tmp,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
\subsection{Read DGINN Table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{dginnT}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
\hlstr{"data/DGINN_202005281649summary_cleaned.csv"}\hlstd{),}
\hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T,} \hlkwc{sep}\hlstd{=}\hlstr{","}\hlstd{)}
\hlkwd{dim}\hlstd{(dginnT)}
\end{alltt}
\begin{verbatim}
## [1] 412 27
\end{verbatim}
\begin{alltt}
\hlkwd{names}\hlstd{(dginnT)}
\end{alltt}
\begin{verbatim}
## [1] "File" "Name" "Gene" "GeneSize" "NbSpecies"
## [6] "omegaM0Bpp" "omegaM0codeml" "BUSTED" "BUSTED.p.value" "MEME.NbSites"
## [11] "MEME.PSS" "BppM1M2" "BppM1M2.p.value" "BppM1M2.NbSites" "BppM1M2.PSS"
## [16] "BppM7M8" "BppM7M8.p.value" "BppM7M8.NbSites" "BppM7M8.PSS" "codemlM1M2"
## [21] "codemlM1M2.p.value" "codemlM1M2.NbSites" "codemlM1M2.PSS" "codemlM7M8" "codemlM7M8.p.value"
## [26] "codemlM7M8.NbSites" "codemlM7M8.PSS"
\end{verbatim}
\begin{alltt}
\hlcom{# Number of genes in dginn-primate output not present in the original table}
\hlstd{dginnT[(dginnT}\hlopt{$}\hlstd{Gene} \hlopt{%in%} \hlstd{tab}\hlopt{$}\hlstd{Gene.name)}\hlopt{==}\hlstd{F,}\hlstr{"Gene"}\hlstd{]}
\end{alltt}
\begin{verbatim}
## [1] ACE2 ADAM9[0-3120] ADAM9[3119-3927] ATP5MGL C1H1ORF50 CEP135[0-3264]
## [7] CEP135[3263-3678] CEP43 COQ8B COQ8A CSNK2A1 CSNK2B[0-609]
## [13] CSNK2B[608-2568] CYB5R1 DDX21[0-717] DDX21[716-2538] DDX50 DNAJC15
## [19] DPH5[0-702] DPH5[701-1326] DPY19L2 ELOC ERO1B EXOSC3[0-1446]
## [25] EXOSC3[1445-1980] FBN3 GNB4 GNB2 GNB3 GOLGA7[0-312]
## [31] GOLGA7[311-549] GPX1[0-1218] GPX1[1217-2946] HDAC1 HS6ST3 IMPDH1
## [37] ITGB1[0-2328] ITGB1[2327-2844] LMAN2L MRPS5[0-1569] MRPS5[1568-3783] MARC2
## [43] MGRN1 NDFIP2[0-768] NDFIP2[767-1314] NDUFAF2[0-258] NDUFAF2[257-744] NSD2
## [49] NUP58 NUP58[0-1824] NUP58[1823-2367] PABPC3 POTPABPC1 PABPC4L
## [55] PABPC5 PCSK5 PRIM2[0-1071] PRIM2[1070-1902] PRKACB PRKACG
## [61] PTGES2[0-1587] PTGES2[1586-2202] RAB8B RAB13 RAB18[0-855] RAB18[854-1815]
## [67] RAB2B RAB5A RAB5B RAB15 RALB EZR
## [73] EZR[0-1458] EZR[1457-3771] MSN RETREG3 RHOB RHOC
## [79] SLC44A2[0-2577] SLC44A2[2576-3657] SPART SRP72[0-2604] SRP72[2603-3417] STOM[0-1047]
## [85] STOM[1046-1800] STOML3 TIMM29 TLE4 TLE2 TLE2[0-1302]
## [91] TLE2[1301-3987] TMPRSS2 TOMM70 TOR1B WASHC4 WFS1[0-2346]
## [97] WFS1[2345-3216] YIF1B
## 411 Levels: AAR2 AASS AATF ABCC1 ACAD9 ACADM ACE2 ACSL3 ADAM9 ADAM9[0-3120] ADAM9[3119-3927] ADAMTS1 AES AGPS AKAP8 ... ZYG11B
\end{verbatim}
\begin{alltt}
\hlcom{# This includes paralogs, recombinations found by DGINN and additionnal genes }
\hlcom{# included on purpose}
\hlcom{# Number of genes from the original list not present in DGINN output}
\hlstd{tab[(tab}\hlopt{$}\hlstd{Gene.name} \hlopt{%in%} \hlstd{dginnT}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlstd{F,}\hlstr{"Gene.name"}\hlstd{]}
\end{alltt}
\begin{verbatim}
## [1] "ADCK4" "ARL6IP6" "ATP5L" "C19orf52" "C1orf50" "ERO1LB" "FAM134C" "FGFR1OP" "KIAA1033" "MFGE8" "NUPL1"
## [12] "SIGMAR1" "SPG20" "TCEB1" "TCEB2" "TOMM70A" "USP13" "VIMP" "WHSC1"
\end{verbatim}
\begin{alltt}
\hlkwd{names}\hlstd{(dginnT)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"Name"}\hlstd{,} \hlstr{"Gene.name"}\hlstd{,} \hlstr{"GeneSize"}\hlstd{,}
\hlstr{"dginn-primate_NbSpecies"}\hlstd{,} \hlstr{"dginn-primate_omegaM0Bpp"}\hlstd{,}
\hlstr{"dginn-primate_omegaM0codeml"}\hlstd{,} \hlstr{"dginn-primate_BUSTED"}\hlstd{,}
\hlstr{"dginn-primate_BUSTED.p.value"}\hlstd{,} \hlstr{"dginn-primate_MEME.NbSites"}\hlstd{,}
\hlstr{"dginn-primate_MEME.PSS"}\hlstd{,} \hlstr{"dginn-primate_BppM1M2"}\hlstd{,}
\hlstr{"dginn-primate_BppM1M2.p.value"}\hlstd{,} \hlstr{"dginn-primate_BppM1M2.NbSites"}\hlstd{,}
\hlstr{"dginn-primate_BppM1M2.PSS"}\hlstd{,} \hlstr{"dginn-primate_BppM7M8"}\hlstd{,}
\hlstr{"dginn-primate_BppM7M8.p.value"}\hlstd{,} \hlstr{"dginn-primate_BppM7M8.NbSites"}\hlstd{,}
\hlstr{"dginn-primate_BppM7M8.PSS"}\hlstd{,} \hlstr{"dginn-primate_codemlM1M2"}\hlstd{,}
\hlstr{"dginn-primate_codemlM1M2.p.value"}\hlstd{,} \hlstr{"dginn-primate_codemlM1M2.NbSites"}\hlstd{,}
\hlstr{"dginn-primate_codemlM1M2.PSS"}\hlstd{,} \hlstr{"dginn-primate_codemlM7M8"}\hlstd{,}
\hlstr{"dginn-primate_codemlM7M8.p.value"}\hlstd{,} \hlstr{"dginn-primate_codemlM7M8.NbSites"}\hlstd{,}
\hlstr{"dginn-primate_codemlM7M8.PSS"}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
\subsection{Join Table and DGINN table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnT,} \hlkwc{by}\hlstd{=}\hlstr{"Gene.name"}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
\end{alltt}
\end{kframe}
\end{knitrout}
\subsection{Add DGINN results on bat dataset}
DGINN results from different analysis.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlcom{# original table}
\hlstd{dginnbats}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
\hlstr{"data/DGINN_202005281339summary_cleaned.tab"}\hlstd{),}
\hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
\hlcom{# rerun on corrected alignment}
\hlstd{dginnbatsnew1}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
\hlstr{"data/DGINN_202011262248_summary.tab"}\hlstd{),}
\hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
\hlstd{dginnbatsnew2}\hlkwb{<-}\hlkwd{read.delim}\hlstd{(}\hlkwd{paste0}\hlstd{(workdir,}
\hlstr{"data/DGINN_202012192053_summary.tab"}\hlstd{),}
\hlkwc{fill}\hlstd{=T,} \hlkwc{h}\hlstd{=T)}
\hlcom{# colomne choice, BUSTED and Bppml form first file, codeml from the other one}
\hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew1}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{omegaM0codeml}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{omegaM0codeml}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM1M2}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM1M2}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM1M2_p.value}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM1M2_p.value}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM1M2_NbSites}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM1M2_NbSites}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM1M2_PSS}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM1M2_PSS}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM7M8}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM7M8}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM7M8_p.value}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM7M8_p.value}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM7M8_NbSites}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM7M8_NbSites}
\hlstd{dginnbatsnew}\hlopt{$}\hlstd{codemlM7M8_PSS}\hlkwb{<-}\hlstd{dginnbatsnew2}\hlopt{$}\hlstd{codemlM7M8_PSS}
\hlcom{####}
\hlcom{## RIPK1 is actually a primat results}
\hlcom{## 1. Take it and put it at the right place}
\hlstd{ripk1}\hlkwb{<-}\hlkwd{as.vector}\hlstd{(dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,])}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_omegaM0Bpp`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_omegaM0Bpp`))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BUSTED.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BUSTED.p.value`))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BppM1M2.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BppM1M2.p.value`))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.p.value`))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.PSS`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_BppM7M8.PSS`))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.p.value`))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.PSS`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM1M2.PSS`))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8.p.value`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8.p.value`))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8.PSS`}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(tab}\hlopt{$}\hlstd{`dginn-primate_codemlM7M8.PSS`))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"GeneSize"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{GeneSize}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_NbSpecies"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{NbSpecies}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_omegaM0Bpp"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{omegaM0Bpp}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_omegaM0codeml"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{omegaM0codeml}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BUSTED"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BUSTED}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BUSTED.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BUSTED_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_MEME.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{MEME_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_MEME.PSS"}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(ripk1}\hlopt{$}\hlstd{MEME_PSS))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM1M2}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM1M2_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM1M2_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM1M2.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM1M2_PSS}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM7M8}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM7M8_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM7M8_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_BppM7M8.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{BppM7M8_PSS}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM1M2}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM1M2_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM1M2_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM1M2.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM1M2_PSS}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM7M8}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.p.value"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM7M8_p.value}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.NbSites"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM7M8_NbSites}
\hlstd{tab[tab}\hlopt{$}\hlstd{Gene.name}\hlopt{==}\hlstr{"RIPK1"}\hlstd{,}\hlstr{"dginn-primate_codemlM7M8.PSS"}\hlstd{]}\hlkwb{<-}\hlstd{ripk1}\hlopt{$}\hlstd{codemlM7M8_PSS}
\hlcom{## 2. Remove it}
\hlstd{dginnbatsnew}\hlkwb{<-}\hlstd{dginnbatsnew[dginnbatsnew}\hlopt{$}\hlstd{Gene}\hlopt{!=}\hlstr{"RIPK1"}\hlstd{,]}
\hlcom{## suppress redundant lines}
\hlstd{dginnbats}\hlkwb{<-}\hlstd{dginnbats[(dginnbats}\hlopt{$}\hlstd{Gene} \hlopt{%in%} \hlstd{dginnbatsnew}\hlopt{$}\hlstd{Gene)}\hlopt{==}\hlnum{FALSE}\hlstd{,]}
\hlkwd{names}\hlstd{(dginnbatsnew)}\hlkwb{<-}\hlkwd{names}\hlstd{(dginnbats)}
\hlcom{##############"}
\hlstd{dginnbatsnew[,}\hlnum{4}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(dginnbatsnew[,}\hlnum{4}\hlstd{])}
\hlstd{dginnbats[,}\hlnum{6}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{6}\hlstd{]))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{dginnbats[,}\hlnum{8}\hlstd{]}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{8}\hlstd{])}
\hlstd{dginnbats[,}\hlnum{12}\hlstd{]}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{12}\hlstd{])}
\hlstd{dginnbats[,}\hlnum{13}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{13}\hlstd{]))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlstd{dginnbats[,}\hlnum{16}\hlstd{]}\hlkwb{<-}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{16}\hlstd{])}
\hlstd{dginnbats[,}\hlnum{17}\hlstd{]}\hlkwb{<-}\hlkwd{as.numeric}\hlstd{(}\hlkwd{as.character}\hlstd{(dginnbats[,}\hlnum{17}\hlstd{]))}
\end{alltt}
{\ttfamily\noindent\color{warningcolor}{\#\# Warning: NAs introduits lors de la conversion automatique}}\begin{alltt}
\hlcom{## replace by new data}
\hlstd{dginnbats}\hlkwb{<-}\hlkwd{rbind}\hlstd{(dginnbats, dginnbatsnew)}
\hlkwd{names}\hlstd{(dginnbats)}\hlkwb{<-}\hlkwd{c}\hlstd{(}\hlstr{"File"}\hlstd{,} \hlstr{"bats_Name"}\hlstd{,} \hlstr{"cooper.batsGene"}\hlstd{,} \hlkwd{paste0}\hlstd{(}\hlstr{"bats_"}\hlstd{,}
\hlkwd{names}\hlstd{(dginnbats)[}\hlopt{-}\hlstd{(}\hlnum{1}\hlopt{:}\hlnum{3}\hlstd{)]))}
\hlkwd{names}\hlstd{(dginnbats)}
\end{alltt}
\begin{verbatim}
## [1] "File" "bats_Name" "cooper.batsGene" "bats_GeneSize"
## [5] "bats_NbSpecies" "bats_omegaM0Bpp" "bats_omegaM0codeml" "bats_BUSTED"
## [9] "bats_BUSTED.p.value" "bats_MEME.NbSites" "bats_MEME.PSS" "bats_BppM1M2"
## [13] "bats_BppM1M2.p.value" "bats_BppM1M2.NbSites" "bats_BppM1M2.PSS" "bats_BppM7M8"
## [17] "bats_BppM7M8.p.value" "bats_BppM7M8.NbSites" "bats_BppM7M8.PSS" "bats_codemlM1M2"
## [21] "bats_codemlM1M2.p.value" "bats_codemlM1M2.NbSites" "bats_codemlM1M2.PSS" "bats_codemlM7M8"
## [25] "bats_codemlM7M8.p.value" "bats_codemlM7M8.NbSites" "bats_codemlM7M8.PSS"
\end{verbatim}
\begin{alltt}
\hlstd{tab}\hlkwb{<-}\hlkwd{merge}\hlstd{(tab,dginnbats,} \hlkwc{by}\hlstd{=}\hlstr{"cooper.batsGene"}\hlstd{,} \hlkwc{all.x}\hlstd{=T)}
\end{alltt}
\end{kframe}
\end{knitrout}
\subsection{Write the new table}
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
\hlkwd{write.table}\hlstd{(tab,} \hlstr{"covid_comp_complete.txt"}\hlstd{,} \hlkwc{row.names}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{quote}\hlstd{=}\hlnum{FALSE}\hlstd{,} \hlkwc{sep}\hlstd{=}\hlstr{"\textbackslash{}t"}\hlstd{)}
\end{alltt}
\end{kframe}
\end{knitrout}
\end{document}