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comparison kinatestid_r/Kinatest-R_part2.R @ 4:2f3df9b1c05b draft

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author jfb
date Tue, 06 Feb 2018 17:16:05 -0500
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3:65f235b5fe14 4:2f3df9b1c05b
1 #test myself: this script should take in amino acids for each of the 9 positions and give out every single combination of those AAs
2
3 #need to do following: fix it so that the accession numbers stay with the substrates,
4 #also the neg false constant is totaly unphos'd Ys found by FASTA-2-CSV system# uniprot
5
6 #HOW MANY: IF THERE'S two aas in each position you get 2^9, so I assume the numbers are:
7 #(number in position-4)*(number in position -3)*(number in position -2)...=total
8 # require(rJava)
9 # require(xlsxjars)
10 # require(xlsx)
11 # # require(readxl)
12
13 View(SDtable)
14 bareSDs<-SDtable[2:21,2:16]
15 goodones<-bareSDs>2
16
17 Positionm7<-which(goodones[,1] %in% TRUE)
18 if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
19 Positionm6<-which(goodones[,2] %in% TRUE)
20 if (length(Positionm6)<1){Positionm6<-which(bareSDs[,2]==max(bareSDs[,2]))}
21 Positionm5<-which(goodones[,3] %in% TRUE)
22 if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
23 Positionm4<-which(goodones[,4] %in% TRUE)
24 if (length(Positionm4)<1){Positionm4<-which(bareSDs[,4]==max(bareSDs[,4]))}
25 Positionm3<-which(goodones[,5] %in% TRUE)
26 if (length(Positionm3)<1){Positionm3<-which(bareSDs[,5]==max(bareSDs[,5]))}
27 Positionm2<-which(goodones[,6] %in% TRUE)
28 if (length(Positionm2)<1){Positionm2<-which(bareSDs[,6]==max(bareSDs[,6]))}
29 Positionm1<-which(goodones[,7] %in% TRUE)
30 if (length(Positionm1)<1){Positionm1<-which(bareSDs[,7]==max(bareSDs[,7]))}
31
32 Positiond0<-which(goodones[,8] %in% TRUE)
33 if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
34
35 Positionp1<-which(goodones[,9] %in% TRUE)
36 if (length(Positionp1)<1){Positionp1<-which(bareSDs[,9]==max(bareSDs[,9]))}
37 Positionp2<-which(goodones[,10] %in% TRUE)
38 if (length(Positionp2)<1){Positionp2<-which(bareSDs[,10]==max(bareSDs[,10]))}
39 Positionp3<-which(goodones[,11] %in% TRUE)
40 if (length(Positionp3)<1){Positionp3<-which(bareSDs[,11]==max(bareSDs[,11]))}
41 Positionp4<-which(goodones[,12] %in% TRUE)
42 if (length(Positionp4)<1){Positionp4<-which(bareSDs[,12]==max(bareSDs[,12]))}
43 Positionp5<-which(goodones[,13] %in% TRUE)
44 if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
45 Positionp6<-which(goodones[,14] %in% TRUE)
46 if (length(Positionp6)<1){Positionp6<-which(bareSDs[,14]==max(bareSDs[,14]))}
47 Positionp7<-which(goodones[,15] %in% TRUE)
48 if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
49
50 aa_props2 <- c("1"="A", "2"="C", "3"="D", "4"="E", "5"="F", "6"="G", "7"="H", "8"="I", "9"="K", "10"="L", "11"="M", "12"="N",
51 "13"="P", "14"="Q", "15"="R", "16"="S", "17"="T", "18"="V", "19"="W", "20"="Y")
52 aa_props2<-c(1="A")
53
54 Positionm7<-sapply(Positionm7, function (x) aa_props2[x])
55 Positionm6<-sapply(Positionm6, function (x) aa_props2[x])
56 Positionm5<-sapply(Positionm5, function (x) aa_props2[x])
57 Positionm4<-sapply(Positionm4, function (x) aa_props2[x])
58 Positionm3<-sapply(Positionm3, function (x) aa_props2[x])
59 Positionm2<-sapply(Positionm2, function (x) aa_props2[x])
60 Positionm1<-sapply(Positionm1, function (x) aa_props2[x])
61 Positiond0<-sapply(Positiond0, function (x) aa_props2[x])
62 Positionp1<-sapply(Positionp1, function (x) aa_props2[x])
63 Positionp2<-sapply(Positionp2, function (x) aa_props2[x])
64 Positionp3<-sapply(Positionp3, function (x) aa_props2[x])
65 Positionp4<-sapply(Positionp4, function (x) aa_props2[x])
66 Positionp5<-sapply(Positionp5, function (x) aa_props2[x])
67 Positionp6<-sapply(Positionp6, function (x) aa_props2[x])
68 Positionp7<-sapply(Positionp7, function (x) aa_props2[x])
69
70
71 # Positionm7<-c("D","H","N","V")
72 # Positionm6<-c("E","V")
73 # Positionm5<-c("D","H")
74 # Positionm4<-c("D","N")
75 # Positionm3<-c("D","E","F","Q")
76 # Positionm2<-c("D","N","Q","S")
77 # Positionm1<-c("F","I","L")
78 # Positiond0<-c("Y")
79 # Positionp1<-c("A","E")
80 # Positionp2<-c("T","S","Q","E")
81 # Positionp3<-c("V")
82 # Positionp4<-c("K")
83 # Positionp5<-c("K")
84 # Positionp6<-c("K")
85 # Positionp7<-c("R")
86 #this is where the amino acids for each position are given. m means minus, p mean plus
87 ########################################
88 # ScreenerFilename<-"C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls"
89
90
91
92
93
94
95
96
97
98
99
100 screaner<-read.csv(ScreenerFilename, header = FALSE, stringsAsFactors = FALSE)
101
102
103 Abl<-screaner[2:25,]
104 Arg<-screaner[27:50,]
105 Btk<-screaner[52:75,]
106 Csk<-screaner[77:100,]
107 Fyn<-screaner[102:125,]
108 Hck<-screaner[127:150,]
109 JAK2<-screaner[152:175,]
110 Lck<-screaner[177:200,]
111 Lyn<-screaner[202:225,]
112 Pyk2<-screaner[227:250,]
113 Src<-screaner[252:275,]
114 Syk<-screaner[277:300,]
115 Yes<-screaner[302:325,]
116
117 #two questions: why are we doing BTK when we already have a bioninformatics page about it?
118 #two I reran everything and only get 96 positions of interest in the SD table
119
120
121
122
123
124
125
126
127
128 #Do_You_want_An_Excel_Output_Questionmark<-"NO"
129 GeneratedPeptidesFile<-"GeneratedPeptidesFile.csv"
130
131
132 # Abl<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 4)
133 # Arg<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 5)
134 # Btk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 6)
135 # Csk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 7)
136 # Fyn<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 8)
137 # Hck<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 9)
138 # JAK2<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 10)
139 # Lck<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 11)
140 # Lyn<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 12)
141 # Pyk2<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 13)
142 # Src<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 14)
143 # Syk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 15)
144 # Yes<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 16)
145 #
146
147
148 "A"=1
149 "C"=2
150 "D"=3
151 "E"=4
152 "F"=5
153 "G"=6
154 "H"=7
155 "I"=8
156 "K"=9
157 "L"=10
158 "M"=11
159 "N"=12
160 "P"=13
161 "Q"=14
162 "R"=15
163 "S"=16
164 "T"=17
165 "V"=18
166 "W"=19
167 "Y"=20
168
169 aa_props <- c("A"=A, "C"=C, "D"=D, "E"=E, "F"=F,"G"=G,"H"=H,"I"=I,"K"=K,"L"=L,"M"=M,"N"=N,"P"=P,"Q"=Q,"R"=R,
170 "S"=S,"T"=T,"V"=V,"W"=W,"Y"=Y,"xY"=Y,"O"=21)
171
172 number15<-sapply(Positionm7, function (x) aa_props[x])
173 number14<-sapply(Positionm6, function (x) aa_props[x])
174 number13<-sapply(Positionm5, function (x) aa_props[x])
175 number1 <- sapply(Positionm4, function (x) aa_props[x])
176 number2 <- sapply(Positionm3, function (x) aa_props[x])
177 number3 <- sapply(Positionm2, function (x) aa_props[x])
178 number4 <- sapply(Positionm1, function (x) aa_props[x])
179 number5 <- sapply(Positiond0, function (x) aa_props[x])
180 number6 <- sapply(Positionp1, function (x) aa_props[x])
181 number7 <- sapply(Positionp2, function (x) aa_props[x])
182 number8 <- sapply(Positionp3, function (x) aa_props[x])
183 number9 <- sapply(Positionp4, function (x) aa_props[x])
184 number10<-sapply(Positionp5, function (x) aa_props[x])
185 number11<-sapply(Positionp6, function (x) aa_props[x])
186 number12<-sapply(Positionp7, function (x) aa_props[x])
187
188 # number1<-Positionm4
189 # number2<-Positionm3
190 # number3<-Positionm2
191 # number4<-Positionm1
192 # number5<-Positiond0
193 # number6<-Positionp1
194 # number7<-Positionp2
195 # number8<-Positionp3
196 # number9<-Positionp4
197
198 #############################
199 #here I create the Abl seqs with proper value for each number
200 if (1==0){
201 Ablnumber1<- gsub("A",A,Ablnumber1,perl = TRUE)
202 Ablnumber1<- gsub("C",C,Ablnumber1,perl = TRUE)
203 Ablnumber1<- gsub("D",D,Ablnumber1,perl = TRUE)
204 Ablnumber1<- gsub("E",E,Ablnumber1,perl = TRUE)
205 Ablnumber1<- gsub("F",F,Ablnumber1,perl = TRUE)
206 Ablnumber1<- gsub("G",G,Ablnumber1,perl = TRUE)
207 Ablnumber1<- gsub("H",H,Ablnumber1,perl = TRUE)
208 Ablnumber1<- gsub("I",I,Ablnumber1,perl = TRUE)
209 Ablnumber1<- gsub("K",K,Ablnumber1,perl = TRUE)
210 Ablnumber1<- gsub("L",L,Ablnumber1,perl = TRUE)
211 Ablnumber1<- gsub("M",M,Ablnumber1,perl = TRUE)
212 Ablnumber1<- gsub("N",N,Ablnumber1,perl = TRUE)
213 Ablnumber1<- gsub("P",P,Ablnumber1,perl = TRUE)
214 Ablnumber1<- gsub("Q",Q,Ablnumber1,perl = TRUE)
215 Ablnumber1<- gsub("R",R,Ablnumber1,perl = TRUE)
216 Ablnumber1<- gsub("S",S,Ablnumber1,perl = TRUE)
217 Ablnumber1<- gsub("T",T,Ablnumber1,perl = TRUE)
218 Ablnumber1<- gsub("V",V,Ablnumber1,perl = TRUE)
219 Ablnumber1<- gsub("W",W,Ablnumber1,perl = TRUE)
220 Ablnumber1<- gsub("Y",Y,Ablnumber1,perl = TRUE)
221
222 Ablnumber2<- gsub("A",A,Ablnumber2,perl = TRUE)
223 Ablnumber2<- gsub("C",C,Ablnumber2,perl = TRUE)
224 Ablnumber2<- gsub("D",D,Ablnumber2,perl = TRUE)
225 Ablnumber2<- gsub("E",E,Ablnumber2,perl = TRUE)
226 Ablnumber2<- gsub("F",F,Ablnumber2,perl = TRUE)
227 Ablnumber2<- gsub("G",G,Ablnumber2,perl = TRUE)
228 Ablnumber2<- gsub("H",H,Ablnumber2,perl = TRUE)
229 Ablnumber2<- gsub("I",I,Ablnumber2,perl = TRUE)
230 Ablnumber2<- gsub("K",K,Ablnumber2,perl = TRUE)
231 Ablnumber2<- gsub("L",L,Ablnumber2,perl = TRUE)
232 Ablnumber2<- gsub("M",M,Ablnumber2,perl = TRUE)
233 Ablnumber2<- gsub("N",N,Ablnumber2,perl = TRUE)
234 Ablnumber2<- gsub("P",P,Ablnumber2,perl = TRUE)
235 Ablnumber2<- gsub("Q",Q,Ablnumber2,perl = TRUE)
236 Ablnumber2<- gsub("R",R,Ablnumber2,perl = TRUE)
237 Ablnumber2<- gsub("S",S,Ablnumber2,perl = TRUE)
238 Ablnumber2<- gsub("T",T,Ablnumber2,perl = TRUE)
239 Ablnumber2<- gsub("V",V,Ablnumber2,perl = TRUE)
240 Ablnumber2<- gsub("W",W,Ablnumber2,perl = TRUE)
241 Ablnumber2<- gsub("Y",Y,Ablnumber2,perl = TRUE)
242
243 Ablnumber3<- gsub("A",A,Ablnumber3,perl = TRUE)
244 Ablnumber3<- gsub("C",C,Ablnumber3,perl = TRUE)
245 Ablnumber3<- gsub("D",D,Ablnumber3,perl = TRUE)
246 Ablnumber3<- gsub("E",E,Ablnumber3,perl = TRUE)
247 Ablnumber3<- gsub("F",F,Ablnumber3,perl = TRUE)
248 Ablnumber3<- gsub("G",G,Ablnumber3,perl = TRUE)
249 Ablnumber3<- gsub("H",H,Ablnumber3,perl = TRUE)
250 Ablnumber3<- gsub("I",I,Ablnumber3,perl = TRUE)
251 Ablnumber3<- gsub("K",K,Ablnumber3,perl = TRUE)
252 Ablnumber3<- gsub("L",L,Ablnumber3,perl = TRUE)
253 Ablnumber3<- gsub("M",M,Ablnumber3,perl = TRUE)
254 Ablnumber3<- gsub("N",N,Ablnumber3,perl = TRUE)
255 Ablnumber3<- gsub("P",P,Ablnumber3,perl = TRUE)
256 Ablnumber3<- gsub("Q",Q,Ablnumber3,perl = TRUE)
257 Ablnumber3<- gsub("R",R,Ablnumber3,perl = TRUE)
258 Ablnumber3<- gsub("S",S,Ablnumber3,perl = TRUE)
259 Ablnumber3<- gsub("T",T,Ablnumber3,perl = TRUE)
260 Ablnumber3<- gsub("V",V,Ablnumber3,perl = TRUE)
261 Ablnumber3<- gsub("W",W,Ablnumber3,perl = TRUE)
262 Ablnumber3<- gsub("Y",Y,Ablnumber3,perl = TRUE)
263
264 Ablnumber4<- gsub("A",A,Ablnumber4,perl = TRUE)
265 Ablnumber4<- gsub("C",C,Ablnumber4,perl = TRUE)
266 Ablnumber4<- gsub("D",D,Ablnumber4,perl = TRUE)
267 Ablnumber4<- gsub("E",E,Ablnumber4,perl = TRUE)
268 Ablnumber4<- gsub("F",F,Ablnumber4,perl = TRUE)
269 Ablnumber4<- gsub("G",G,Ablnumber4,perl = TRUE)
270 Ablnumber4<- gsub("H",H,Ablnumber4,perl = TRUE)
271 Ablnumber4<- gsub("I",I,Ablnumber4,perl = TRUE)
272 Ablnumber4<- gsub("K",K,Ablnumber4,perl = TRUE)
273 Ablnumber4<- gsub("L",L,Ablnumber4,perl = TRUE)
274 Ablnumber4<- gsub("M",M,Ablnumber4,perl = TRUE)
275 Ablnumber4<- gsub("N",N,Ablnumber4,perl = TRUE)
276 Ablnumber4<- gsub("P",P,Ablnumber4,perl = TRUE)
277 Ablnumber4<- gsub("Q",Q,Ablnumber4,perl = TRUE)
278 Ablnumber4<- gsub("R",R,Ablnumber4,perl = TRUE)
279 Ablnumber4<- gsub("S",S,Ablnumber4,perl = TRUE)
280 Ablnumber4<- gsub("T",T,Ablnumber4,perl = TRUE)
281 Ablnumber4<- gsub("V",V,Ablnumber4,perl = TRUE)
282 Ablnumber4<- gsub("W",W,Ablnumber4,perl = TRUE)
283 Ablnumber4<- gsub("Y",Y,Ablnumber4,perl = TRUE)
284
285 Ablnumber5<- gsub("A",A,Ablnumber5,perl = TRUE)
286 Ablnumber5<- gsub("C",C,Ablnumber5,perl = TRUE)
287 Ablnumber5<- gsub("D",D,Ablnumber5,perl = TRUE)
288 Ablnumber5<- gsub("E",E,Ablnumber5,perl = TRUE)
289 Ablnumber5<- gsub("F",F,Ablnumber5,perl = TRUE)
290 Ablnumber5<- gsub("G",G,Ablnumber5,perl = TRUE)
291 Ablnumber5<- gsub("H",H,Ablnumber5,perl = TRUE)
292 Ablnumber5<- gsub("I",I,Ablnumber5,perl = TRUE)
293 Ablnumber5<- gsub("K",K,Ablnumber5,perl = TRUE)
294 Ablnumber5<- gsub("L",L,Ablnumber5,perl = TRUE)
295 Ablnumber5<- gsub("M",M,Ablnumber5,perl = TRUE)
296 Ablnumber5<- gsub("N",N,Ablnumber5,perl = TRUE)
297 Ablnumber5<- gsub("P",P,Ablnumber5,perl = TRUE)
298 Ablnumber5<- gsub("Q",Q,Ablnumber5,perl = TRUE)
299 Ablnumber5<- gsub("R",R,Ablnumber5,perl = TRUE)
300 Ablnumber5<- gsub("S",S,Ablnumber5,perl = TRUE)
301 Ablnumber5<- gsub("T",T,Ablnumber5,perl = TRUE)
302 Ablnumber5<- gsub("V",V,Ablnumber5,perl = TRUE)
303 Ablnumber5<- gsub("W",W,Ablnumber5,perl = TRUE)
304 Ablnumber5<- gsub("Y",Y,Ablnumber5,perl = TRUE)
305
306 Ablnumber6<- gsub("A",A,Ablnumber6,perl = TRUE)
307 Ablnumber6<- gsub("C",C,Ablnumber6,perl = TRUE)
308 Ablnumber6<- gsub("D",D,Ablnumber6,perl = TRUE)
309 Ablnumber6<- gsub("E",E,Ablnumber6,perl = TRUE)
310 Ablnumber6<- gsub("F",F,Ablnumber6,perl = TRUE)
311 Ablnumber6<- gsub("G",G,Ablnumber6,perl = TRUE)
312 Ablnumber6<- gsub("H",H,Ablnumber6,perl = TRUE)
313 Ablnumber6<- gsub("I",I,Ablnumber6,perl = TRUE)
314 Ablnumber6<- gsub("K",K,Ablnumber6,perl = TRUE)
315 Ablnumber6<- gsub("L",L,Ablnumber6,perl = TRUE)
316 Ablnumber6<- gsub("M",M,Ablnumber6,perl = TRUE)
317 Ablnumber6<- gsub("N",N,Ablnumber6,perl = TRUE)
318 Ablnumber6<- gsub("P",P,Ablnumber6,perl = TRUE)
319 Ablnumber6<- gsub("Q",Q,Ablnumber6,perl = TRUE)
320 Ablnumber6<- gsub("R",R,Ablnumber6,perl = TRUE)
321 Ablnumber6<- gsub("S",S,Ablnumber6,perl = TRUE)
322 Ablnumber6<- gsub("T",T,Ablnumber6,perl = TRUE)
323 Ablnumber6<- gsub("V",V,Ablnumber6,perl = TRUE)
324 Ablnumber6<- gsub("W",W,Ablnumber6,perl = TRUE)
325 Ablnumber6<- gsub("Y",Y,Ablnumber6,perl = TRUE)
326
327 Ablnumber7<- gsub("A",A,Ablnumber7,perl = TRUE)
328 Ablnumber7<- gsub("C",C,Ablnumber7,perl = TRUE)
329 Ablnumber7<- gsub("D",D,Ablnumber7,perl = TRUE)
330 Ablnumber7<- gsub("E",E,Ablnumber7,perl = TRUE)
331 Ablnumber7<- gsub("F",F,Ablnumber7,perl = TRUE)
332 Ablnumber7<- gsub("G",G,Ablnumber7,perl = TRUE)
333 Ablnumber7<- gsub("H",H,Ablnumber7,perl = TRUE)
334 Ablnumber7<- gsub("I",I,Ablnumber7,perl = TRUE)
335 Ablnumber7<- gsub("K",K,Ablnumber7,perl = TRUE)
336 Ablnumber7<- gsub("L",L,Ablnumber7,perl = TRUE)
337 Ablnumber7<- gsub("M",M,Ablnumber7,perl = TRUE)
338 Ablnumber7<- gsub("N",N,Ablnumber7,perl = TRUE)
339 Ablnumber7<- gsub("P",P,Ablnumber7,perl = TRUE)
340 Ablnumber7<- gsub("Q",Q,Ablnumber7,perl = TRUE)
341 Ablnumber7<- gsub("R",R,Ablnumber7,perl = TRUE)
342 Ablnumber7<- gsub("S",S,Ablnumber7,perl = TRUE)
343 Ablnumber7<- gsub("T",T,Ablnumber7,perl = TRUE)
344 Ablnumber7<- gsub("V",V,Ablnumber7,perl = TRUE)
345 Ablnumber7<- gsub("W",W,Ablnumber7,perl = TRUE)
346 Ablnumber7<- gsub("Y",Y,Ablnumber7,perl = TRUE)
347
348 Ablnumber8<- gsub("A",A,Ablnumber8,perl = TRUE)
349 Ablnumber8<- gsub("C",C,Ablnumber8,perl = TRUE)
350 Ablnumber8<- gsub("D",D,Ablnumber8,perl = TRUE)
351 Ablnumber8<- gsub("E",E,Ablnumber8,perl = TRUE)
352 Ablnumber8<- gsub("F",F,Ablnumber8,perl = TRUE)
353 Ablnumber8<- gsub("G",G,Ablnumber8,perl = TRUE)
354 Ablnumber8<- gsub("H",H,Ablnumber8,perl = TRUE)
355 Ablnumber8<- gsub("I",I,Ablnumber8,perl = TRUE)
356 Ablnumber8<- gsub("K",K,Ablnumber8,perl = TRUE)
357 Ablnumber8<- gsub("L",L,Ablnumber8,perl = TRUE)
358 Ablnumber8<- gsub("M",M,Ablnumber8,perl = TRUE)
359 Ablnumber8<- gsub("N",N,Ablnumber8,perl = TRUE)
360 Ablnumber8<- gsub("P",P,Ablnumber8,perl = TRUE)
361 Ablnumber8<- gsub("Q",Q,Ablnumber8,perl = TRUE)
362 Ablnumber8<- gsub("R",R,Ablnumber8,perl = TRUE)
363 Ablnumber8<- gsub("S",S,Ablnumber8,perl = TRUE)
364 Ablnumber8<- gsub("T",T,Ablnumber8,perl = TRUE)
365 Ablnumber8<- gsub("V",V,Ablnumber8,perl = TRUE)
366 Ablnumber8<- gsub("W",W,Ablnumber8,perl = TRUE)
367 Ablnumber8<- gsub("Y",Y,Ablnumber8,perl = TRUE)
368
369 Ablnumber9<- gsub("A",A,Ablnumber9,perl = TRUE)
370 Ablnumber9<- gsub("C",C,Ablnumber9,perl = TRUE)
371 Ablnumber9<- gsub("D",D,Ablnumber9,perl = TRUE)
372 Ablnumber9<- gsub("E",E,Ablnumber9,perl = TRUE)
373 Ablnumber9<- gsub("F",F,Ablnumber9,perl = TRUE)
374 Ablnumber9<- gsub("G",G,Ablnumber9,perl = TRUE)
375 Ablnumber9<- gsub("H",H,Ablnumber9,perl = TRUE)
376 Ablnumber9<- gsub("I",I,Ablnumber9,perl = TRUE)
377 Ablnumber9<- gsub("K",K,Ablnumber9,perl = TRUE)
378 Ablnumber9<- gsub("L",L,Ablnumber9,perl = TRUE)
379 Ablnumber9<- gsub("M",M,Ablnumber9,perl = TRUE)
380 Ablnumber9<- gsub("N",N,Ablnumber9,perl = TRUE)
381 Ablnumber9<- gsub("P",P,Ablnumber9,perl = TRUE)
382 Ablnumber9<- gsub("Q",Q,Ablnumber9,perl = TRUE)
383 Ablnumber9<- gsub("R",R,Ablnumber9,perl = TRUE)
384 Ablnumber9<- gsub("S",S,Ablnumber9,perl = TRUE)
385 Ablnumber9<- gsub("T",T,Ablnumber9,perl = TRUE)
386 Ablnumber9<- gsub("V",V,Ablnumber9,perl = TRUE)
387 Ablnumber9<- gsub("W",W,Ablnumber9,perl = TRUE)
388 Ablnumber9<- gsub("Y",Y,Ablnumber9,perl = TRUE)
389 }
390 ########################################
391
392
393 total=length(Positionp7)*length(Positionp6)*length(Positionp5)*length(Positionp4)*length(Positionp3)*(length(Positionp2))*length(Positionp1)*
394 length(Positiond0)*length(Positionm1)*length(Positionm2)*length(Positionm3)*length(Positionm4)*length(Positionm5)*length(Positionm6)*length(Positionm7)
395 #this is just a way to doublecheck that the length of the generated peptides vector is correct
396
397 GeneratedPeptides<-rep(NA, times=total*15)
398 GeneratedPeptides<-matrix(data = GeneratedPeptides,ncol = 15)
399
400 NumeratedPeptides<-GeneratedPeptides
401 #create an empty vector of correct length by finding the number of each AAs per position and multiplying them
402 count<-0
403 for (t in 1:length(Positionm7)) {
404 for (s in 1:length(Positionm6)) {
405 for (r in 1:length(Positionm5)) {
406 for (i in 1:length(Positionm4)) {
407 for (j in 1:length(Positionm3)) {
408 for (k in 1:length(Positionm2)) {
409 for (l in 1:length(Positionm1)) {
410 for (m in 1:length(Positiond0)) {
411 for (n in 1:length(Positionp1)) {
412 for (o in 1:length(Positionp2)) {
413 for (p in 1:length(Positionp3)) {
414 for (q in 1:length(Positionp4)) {
415 for (u in 1:length(Positionp5)) {
416 for (v in 1:length(Positionp6)) {
417 for (w in 1:length(Positionp7)) {
418 # i=1
419 # j=1
420 # k=1
421 # l=1
422 # m=1
423 # n=1
424 # o=1
425 # p=1
426 # q=1
427 #
428 #for every single position, increment the count number, create a peptide using the AAs at that position
429 #then put them together into the generated peptides sequencex
430 count<-count+1
431 tabulation<-c(Positionm7[t],Positionm6[s],Positionm5[r],Positionm4[i],Positionm3[j],Positionm2[k],Positionm1[l],Positiond0[m],Positionp1[n],
432 Positionp2[o],Positionp3[p],Positionp4[q],Positionp5[u],Positionp6[v],Positionp7[w])
433 numeration<-c(number15[t],number14[s],number13[r],number1[i],number2[j],number3[k],number4[l],number5[m],number6[n],number7[o],number8[p],number9[q],number10[u],number11[v],
434 number12[w])
435 #tabulation<-paste(tabulation, sep="", collapse="")
436 GeneratedPeptides[count,1:15]<-tabulation
437 NumeratedPeptides[count,1:15]<-numeration
438 }
439 }
440 }
441 }
442 }
443 }
444 }
445 }
446 }
447 }
448 }
449 }
450 }
451 }
452 }
453 ####################################################################
454 #now here I use the Endogenous Probabilty matrix from the previous script, which is called EMPtable
455 #to score the created peptides
456 ThisKinTable<-EPMtableu#[1:nrow(SDtable),]
457 TKTcolumn<-c(data=rep(1,times=21))
458 TKTcolumn<-as.matrix(TKTcolumn,ncol=1)
459 ThisKinTable<-cbind(TKTcolumn,ThisKinTable)
460
461 ThisKinGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
462 ThisKinGenWeirdScore<-rep(NA,times=nrow(GeneratedPeptides))
463
464 for (x in 1:nrow(GeneratedPeptides)){
465 Scoringpeptide<-NumeratedPeptides[x,1:15]
466 Scoringpeptide<-Scoringpeptide+1
467 ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
468 ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]*
469 #ThisKinTable[as.numeric(Scoringpeptide[8]),10]*
470 ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]*
471 ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17]
472 ThisKinGeneratedScores[x]<-ThisKinTableScore
473 ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2])))
474 ThisKinGenWeirdScore[x]<-ThisKinTableScore
475 }
476
477 AblGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
478 ArgGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
479 BtkGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
480 CskGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
481 FynGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
482 HckGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
483 JAK2GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
484 LckGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
485 LynGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
486 Pyk2GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
487 SrcGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
488 SykGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
489 YesGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
490
491
492 for (x in 1:nrow(GeneratedPeptides)){
493 Scoringpeptide<-NumeratedPeptides[x,1:15]
494 AblScore<-Abl[Scoringpeptide[1],2]*Abl[Scoringpeptide[2],3]*Abl[Scoringpeptide[3],4]*Abl[Scoringpeptide[4],5]*Abl[Scoringpeptide[5],6]*Abl[Scoringpeptide[6],7]*
495 Abl[Scoringpeptide[7],8]*Abl[Scoringpeptide[9],10]*Abl[Scoringpeptide[10],11]*Abl[Scoringpeptide[11],12]*Abl[Scoringpeptide[12],13]*
496 Abl[Scoringpeptide[13],14]*Abl[Scoringpeptide[14],15]*Abl[Scoringpeptide[15],16]
497 AblGeneratedScores[x]<-AblScore
498
499 ArgScore<-Arg[Scoringpeptide[1],2]*Arg[Scoringpeptide[2],3]*Arg[Scoringpeptide[3],4]*Arg[Scoringpeptide[4],5]*Arg[Scoringpeptide[5],6]*Arg[Scoringpeptide[6],7]*
500 Arg[Scoringpeptide[7],8]*Arg[Scoringpeptide[9],10]*Arg[Scoringpeptide[10],11]*Arg[Scoringpeptide[11],12]*Arg[Scoringpeptide[12],13]*
501 Arg[Scoringpeptide[13],14]*Arg[Scoringpeptide[14],15]*Arg[Scoringpeptide[15],16]
502 ArgGeneratedScores[x]<-ArgScore
503
504 BtkScore<-Btk[Scoringpeptide[1],2]*Btk[Scoringpeptide[2],3]*Btk[Scoringpeptide[3],4]*Btk[Scoringpeptide[4],5]*Btk[Scoringpeptide[5],6]*Btk[Scoringpeptide[6],7]*
505 Btk[Scoringpeptide[7],8]*Btk[Scoringpeptide[9],10]*Btk[Scoringpeptide[10],11]*Btk[Scoringpeptide[11],12]*Btk[Scoringpeptide[12],13]*
506 Btk[Scoringpeptide[13],14]*Btk[Scoringpeptide[14],15]*Btk[Scoringpeptide[15],16]
507 BtkGeneratedScores[x]<-BtkScore
508
509 CskScore<-Csk[Scoringpeptide[1],2]*Csk[Scoringpeptide[2],3]*Csk[Scoringpeptide[3],4]*Csk[Scoringpeptide[4],5]*Csk[Scoringpeptide[5],6]*Csk[Scoringpeptide[6],7]*
510 Csk[Scoringpeptide[7],8]*Csk[Scoringpeptide[9],10]*Csk[Scoringpeptide[10],11]*Csk[Scoringpeptide[11],12]*Csk[Scoringpeptide[12],13]*
511 Csk[Scoringpeptide[13],14]*Csk[Scoringpeptide[14],15]*Csk[Scoringpeptide[15],16]
512 CskGeneratedScores[x]<-CskScore
513
514 FynScore<-Fyn[Scoringpeptide[1],2]*Fyn[Scoringpeptide[2],3]*Fyn[Scoringpeptide[3],4]*Fyn[Scoringpeptide[4],5]*Fyn[Scoringpeptide[5],6]*Fyn[Scoringpeptide[6],7]*
515 Fyn[Scoringpeptide[7],8]*Fyn[Scoringpeptide[9],10]*Fyn[Scoringpeptide[10],11]*Fyn[Scoringpeptide[11],12]*Fyn[Scoringpeptide[12],13]*
516 Fyn[Scoringpeptide[13],14]*Fyn[Scoringpeptide[14],15]*Fyn[Scoringpeptide[15],16]
517 FynGeneratedScores[x]<-FynScore
518
519 HckScore<-Hck[Scoringpeptide[1],2]*Hck[Scoringpeptide[2],3]*Hck[Scoringpeptide[3],4]*Hck[Scoringpeptide[4],5]*Hck[Scoringpeptide[5],6]*Hck[Scoringpeptide[6],7]*
520 Hck[Scoringpeptide[7],8]*Hck[Scoringpeptide[9],10]*Hck[Scoringpeptide[10],11]*Hck[Scoringpeptide[11],12]*Hck[Scoringpeptide[12],13]*
521 Hck[Scoringpeptide[13],14]*Hck[Scoringpeptide[14],15]*Hck[Scoringpeptide[15],16]
522 HckGeneratedScores[x]<-HckScore
523
524 JAK2Score<-JAK2[Scoringpeptide[1],2]*JAK2[Scoringpeptide[2],3]*JAK2[Scoringpeptide[3],4]*JAK2[Scoringpeptide[4],5]*JAK2[Scoringpeptide[5],6]*JAK2[Scoringpeptide[6],7]*
525 JAK2[Scoringpeptide[7],8]*JAK2[Scoringpeptide[9],10]*JAK2[Scoringpeptide[10],11]*JAK2[Scoringpeptide[11],12]*JAK2[Scoringpeptide[12],13]*
526 JAK2[Scoringpeptide[13],14]*JAK2[Scoringpeptide[14],15]*JAK2[Scoringpeptide[15],16]
527 JAK2GeneratedScores[x]<-JAK2Score
528
529 LckScore<-Lck[Scoringpeptide[1],2]*Lck[Scoringpeptide[2],3]*Lck[Scoringpeptide[3],4]*Lck[Scoringpeptide[4],5]*Lck[Scoringpeptide[5],6]*Lck[Scoringpeptide[6],7]*
530 Lck[Scoringpeptide[7],8]*Lck[Scoringpeptide[9],10]*Lck[Scoringpeptide[10],11]*Lck[Scoringpeptide[11],12]*Lck[Scoringpeptide[12],13]*
531 Lck[Scoringpeptide[13],14]*Lck[Scoringpeptide[14],15]*Lck[Scoringpeptide[15],16]
532 LckGeneratedScores[x]<-LckScore
533
534 LynScore<-Lyn[Scoringpeptide[1],2]*Lyn[Scoringpeptide[2],3]*Lyn[Scoringpeptide[3],4]*Lyn[Scoringpeptide[4],5]*Lyn[Scoringpeptide[5],6]*Lyn[Scoringpeptide[6],7]*
535 Lyn[Scoringpeptide[7],8]*Lyn[Scoringpeptide[9],10]*Lyn[Scoringpeptide[10],11]*Lyn[Scoringpeptide[11],12]*Lyn[Scoringpeptide[12],13]*
536 Lyn[Scoringpeptide[13],14]*Lyn[Scoringpeptide[14],15]*Lyn[Scoringpeptide[15],16]
537 LynGeneratedScores[x]<-LynScore
538
539 Pyk2Score<-Pyk2[Scoringpeptide[1],2]*Pyk2[Scoringpeptide[2],3]*Pyk2[Scoringpeptide[3],4]*Pyk2[Scoringpeptide[4],5]*Pyk2[Scoringpeptide[5],6]*Pyk2[Scoringpeptide[6],7]*
540 Pyk2[Scoringpeptide[7],8]*Pyk2[Scoringpeptide[9],10]*Pyk2[Scoringpeptide[10],11]*Pyk2[Scoringpeptide[11],12]*Pyk2[Scoringpeptide[12],13]*
541 Pyk2[Scoringpeptide[13],14]*Pyk2[Scoringpeptide[14],15]*Pyk2[Scoringpeptide[15],16]
542 Pyk2GeneratedScores[x]<-Pyk2Score
543
544 SrcScore<-Src[Scoringpeptide[1],2]*Src[Scoringpeptide[2],3]*Src[Scoringpeptide[3],4]*Src[Scoringpeptide[4],5]*Src[Scoringpeptide[5],6]*Src[Scoringpeptide[6],7]*
545 Src[Scoringpeptide[7],8]*Src[Scoringpeptide[9],10]*Src[Scoringpeptide[10],11]*Src[Scoringpeptide[11],12]*Src[Scoringpeptide[12],13]*
546 Src[Scoringpeptide[13],14]*Src[Scoringpeptide[14],15]*Src[Scoringpeptide[15],16]
547 SrcGeneratedScores[x]<-SrcScore
548
549 SykScore<-Syk[Scoringpeptide[1],2]*Syk[Scoringpeptide[2],3]*Syk[Scoringpeptide[3],4]*Syk[Scoringpeptide[4],5]*Syk[Scoringpeptide[5],6]*Syk[Scoringpeptide[6],7]*
550 Syk[Scoringpeptide[7],8]*Syk[Scoringpeptide[9],10]*Syk[Scoringpeptide[10],11]*Syk[Scoringpeptide[11],12]*Syk[Scoringpeptide[12],13]*
551 Syk[Scoringpeptide[13],14]*Syk[Scoringpeptide[14],15]*Syk[Scoringpeptide[15],16]
552 SykGeneratedScores[x]<-SykScore
553
554 YesScore<-Yes[Scoringpeptide[1],2]*Yes[Scoringpeptide[2],3]*Yes[Scoringpeptide[3],4]*Yes[Scoringpeptide[4],5]*Yes[Scoringpeptide[5],6]*Yes[Scoringpeptide[6],7]*
555 Yes[Scoringpeptide[7],8]*Yes[Scoringpeptide[9],10]*Yes[Scoringpeptide[10],11]*Yes[Scoringpeptide[11],12]*Yes[Scoringpeptide[12],13]*
556 Yes[Scoringpeptide[13],14]*Yes[Scoringpeptide[14],15]*Yes[Scoringpeptide[15],16]
557 YesGeneratedScores[x]<-YesScore
558
559 # ThisKinTableScore<-ThisKinTable[as.numeric(Scoringpeptide[1]),3]*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
560 # ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*
561 # ThisKinTable[as.numeric(Scoringpeptide[7]),9]*ThisKinTable[as.numeric(Scoringpeptide[8]),10]*ThisKinTable[as.numeric(Scoringpeptide[9]),11]
562 # ThisKinGeneratedScores[x]<-ThisKinTableScore
563 }
564
565
566
567 AblNorm<-1/as.numeric(Abl[22,1])
568 AblThresh<-as.numeric(Abl[24,1])
569 AblTrueThresh<-((AblThresh*AblNorm)/(100-AblThresh))
570 AblActive<-unlist(AblGeneratedScores)>AblTrueThresh
571
572 ArgNorm<-1/as.numeric(Arg[22,1])
573 ArgThresh<-as.numeric(Arg[24,1])
574 ArgTrueThresh<-((ArgThresh*ArgNorm)/(100-ArgThresh))
575 ArgActive<-unlist(ArgGeneratedScores)>ArgTrueThresh
576
577 BtkNorm<-1/as.numeric(Btk[22,1])
578 BtkThresh<-as.numeric(Btk[24,1])
579 BtkTrueThresh<-((BtkThresh*BtkNorm)/(100-BtkThresh))
580 BtkActive<-unlist(BtkGeneratedScores)>BtkTrueThresh
581
582 CskNorm<-1/as.numeric(Csk[22,1])
583 CskThresh<-as.numeric(Csk[24,1])
584 CskTrueThresh<-((CskThresh*CskNorm)/(100-CskThresh))
585 CskActive<-(CskGeneratedScores)>CskTrueThresh
586
587 FynNorm<-1/as.numeric(Fyn[22,1])
588 FynThresh<-as.numeric(Fyn[24,1])
589 FynTrueThresh<-((FynThresh*FynNorm)/(100-FynThresh))
590 FynActive<-unlist(FynGeneratedScores)>FynTrueThresh
591
592 HckNorm<-1/as.numeric(Hck[22,1])
593 HckThresh<-as.numeric(Hck[24,1])
594 HckTrueThresh<-((HckThresh*HckNorm)/(100-HckThresh))
595 HckActive<-unlist(HckGeneratedScores)>HckTrueThresh
596
597 JAK2Norm<-1/as.numeric(JAK2[22,1])
598 JAK2Thresh<-as.numeric(JAK2[24,1])
599 JAK2TrueThresh<-((JAK2Thresh*JAK2Norm)/(100-JAK2Thresh))
600 JAk2Active<-unlist(JAK2GeneratedScores)>JAK2TrueThresh
601
602 LckNorm<-1/as.numeric(Lck[22,1])
603 LckThresh<-as.numeric(Lck[24,1])
604 LckTrueThresh<-((LckThresh*LckNorm)/(100-LckThresh))
605 LckActive<-unlist(LckGeneratedScores)>LckTrueThresh
606
607 LynNorm<-1/as.numeric(Lyn[22,1])
608 LynThresh<-as.numeric(Lyn[24,1])
609 LynTrueThresh<-((LynThresh*LynNorm)/(100-LynThresh))
610 LynActive<-unlist(LynGeneratedScores)>LynTrueThresh
611
612 Pyk2Norm<-1/as.numeric(Pyk2[22,1])
613 Pyk2Thresh<-as.numeric(Pyk2[24,1])
614 Pyk2TrueThresh<-((Pyk2Thresh*Pyk2Norm)/(100-Pyk2Thresh))
615 Pyk2Active<-unlist(Pyk2GeneratedScores)>Pyk2TrueThresh
616
617 SrcNorm<-1/as.numeric(Src[22,1])
618 SrcThresh<-as.numeric(Src[24,1])
619 SrcTrueThresh<-((SrcThresh*SrcNorm)/(100-SrcThresh))
620 SrcActive<-unlist(SrcGeneratedScores)>SrcTrueThresh
621
622 SykNorm<-1/as.numeric(Syk[22,1])
623 SykThresh<-as.numeric(Syk[24,1])
624 SykTrueThresh<-((SykThresh*SykNorm)/(100-SykThresh))
625 SykActive<-unlist(SykGeneratedScores)>SykTrueThresh
626
627 YesNorm<-1/as.numeric(Yes[22,1])
628 YesThresh<-as.numeric(Yes[24,1])
629 YesTrueThresh<-((YesThresh*YesNorm)/(100-YesThresh))
630 YesActive<-unlist(YesGeneratedScores)>YesTrueThresh
631
632 AllActive<-AblActive+ArgActive+BtkActive+CskActive+FynActive+HckActive+JAk2Active+LckActive+LynActive+Pyk2Active+SrcActive+SykActive+YesActive
633 #Btkactive+
634
635 Scores<-ThisKinGeneratedScores
636 ThresholdValues<-ThisKinGenWeirdScore
637
638 FullMotifs<-rep("Z",times=nrow(GeneratedPeptides))
639 for (i in 1:nrow(GeneratedPeptides)) {
640 motif<-GeneratedPeptides[i,1:15]
641 motif<-paste(motif,sep = "", collapse = "")
642 FullMotifs[i]<-motif
643 }
644
645 PeptidesWithRanks<-cbind.data.frame(FullMotifs,GeneratedPeptides,Scores,ThresholdValues)
646 PeptidesWithRanks<-cbind.data.frame(PeptidesWithRanks,AllActive,AblActive,ArgActive,BtkActive,CskActive,FynActive,HckActive,JAk2Active,LckActive,LynActive,Pyk2Active,SrcActive,SykActive,YesActive)
647 RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks$AllActive,decreasing = FALSE),]
648 # PepRankHead<-c(1:9,"Sequence","RPMS","PMS")
649 # RanksPeptides<-rbind.data.frame(PepRankHead,PeptidesWithRanks)
650 head(RanksPeptides)
651
652
653 #now I have to score the negative sequences... for some reason
654 #write up how we transfect with lipofectamine
655 #3,4,5 questions
656
657 #PAUSED EHRE AT 4:50, HOPING THAT FIXING MINERVOTHING SO THAT LEFT SPACES WORKS FIXES A THING. OTHERWISE
658 #I FUCKED WITH THE MCC TABLE AND NEED TO FINISH IT
659
660 ThisKinBlanks<-rep(1,times=17)
661 ThisKinTable<-rbind(ThisKinTable,ThisKinBlanks)
662
663 NegativeScores<-rep(NA,times=nrow(NegativeSubstrateList))
664 NegativeWeirdScores<-rep(NA,times=nrow(NegativeSubstrateList))
665 for (v in 1:nrow(NegativeSubstrateList)) {
666 motif<-NegativeSubstrateList[v,2]
667 motif<-unlist(strsplit(motif,""))
668 #if (length(motif)<9){print(v)}}
669 # motif[1] <- sapply(motif[1], function (x) aa_props[x])
670 # motif[2] <- sapply(motif[2], function (x) aa_props[x])
671 # motif[3] <- sapply(motif[3], function (x) aa_props[x])
672 # motif[4] <- sapply(motif[4], function (x) aa_props[x])
673 # motif[5] <- sapply(motif[5], function (x) aa_props[x])
674 # motif[6] <- sapply(motif[6], function (x) aa_props[x])
675 # motif[7] <- sapply(motif[7], function (x) aa_props[x])
676 # motif[8] <- sapply(motif[8], function (x) aa_props[x])
677 # motif[9] <- sapply(motif[9], function (x) aa_props[x])
678 motif<- gsub(" ","O",motif)
679 motif <- sapply(motif, function (x) aa_props[x])
680 Scoringpeptide<-motif
681 Scoringpeptide<-Scoringpeptide+1
682 ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
683 ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]*
684 #ThisKinTable[as.numeric(Scoringpeptide[8]),10]*
685 ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]*
686 ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17]
687 NegativeScores[v]<-ThisKinTableScore
688 ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2])))
689 NegativeWeirdScores[v]<-ThisKinTableScore*100
690 }
691
692 negativesubstrates<-NegativeSubstrateList[,2]
693 NegativeWithScores<-cbind(negativesubstrates,as.character(NegativeScores),as.character(NegativeWeirdScores))
694
695
696 #NEED TO HAVE THE NEGATIVE SUBSTRATES BE OUTPUTTED
697
698 PositiveScores<-rep(NA,times=nrow(ImportedSubstrateList))
699 PositiveWeirdScores<-rep(NA,times=nrow(ImportedSubstrateList))
700
701 for (v in 1:nrow(ImportedSubstrateList)) {
702 motif<-ImportedSubstrateList[v,4:18]
703 motif<-unlist(motif)
704 motif<- gsub("^$","O",motif)
705 motif <- sapply(motif, function (x) aa_props[x])
706 Scoringpeptide<-motif
707 Scoringpeptide<-Scoringpeptide+1
708 ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
709 ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]*
710 #ThisKinTable[as.numeric(Scoringpeptide[8]),10]*
711 ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]*
712 ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17]
713
714 PositiveScores[v]<-ThisKinTableScore
715 ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2])))
716 PositiveWeirdScores[v]<-ThisKinTableScore*100
717 }
718
719 positivesubstrates<-ImportedSubstrateList[,4:18]
720 positivewithscores<-cbind.data.frame(positivesubstrates,PositiveScores,PositiveWeirdScores)
721
722
723 #write down the transient transfection SOP and what we will be doing with them
724 #write down the vector names I will be using
725 #write down something about transforming bacteria and with what
726
727 #90% whatevernness
728 # TPninetyone<-length(PositiveWeirdScores[PositiveWeirdScores>=0.91])
729 # Senseninetyone<-TPninetyone/nrow(positivesubstrates)
730 #
731 # TNninetyone<-length(NegativeWeirdScores[NegativeWeirdScores<91])
732 # Specninetyone<-TNninetyone/100
733
734 #create the MCC table
735
736 threshold<-c(1:100)
737 threshold<-order(threshold,decreasing = TRUE)
738
739 Truepositives<-c(1:100)
740 Falsenegatives<-c(1:100)
741 Sensitivity<-c(1:100)
742 TrueNegatives<-c(1:100)
743 FalsePositives<-c(1:100)
744 Specificity<-c(1:100)
745 Accuracy<-c(1:100)
746 MCC<-c(1:100)
747 EER<-c(1:100)
748
749 #MAKE DAMN SURE THAT THE ACCESSION NUMBERS FOLLOW THE MOTIFS
750
751 for (z in 1:100) {
752 thres<-101-z
753 Truepositives[z]<-length(PositiveWeirdScores[PositiveWeirdScores>=(thres)])
754 Falsenegatives[z]<-nrow(positivesubstrates)-Truepositives[z]
755 Sensitivity[z]<-Truepositives[z]/(Falsenegatives[z]+Truepositives[z])
756 TrueNegatives[z]<-length(NegativeWeirdScores[NegativeWeirdScores<(thres)])
757 # at thresh 100 this should be 0, because it is total minus true negatives
758 FalsePositives[z]<-nrow(NegativeSubstrateList)-TrueNegatives[z]
759 Specificity[z]<-1-(TrueNegatives[z]/(FalsePositives[z]+TrueNegatives[z]))
760 Accuracy[z]<-100*(Truepositives[z]+TrueNegatives[z])/(Falsenegatives[z]+FalsePositives[z]+TrueNegatives[z]+Truepositives[z])
761 MCC[z]<-((Truepositives[z]+TrueNegatives[z])-(Falsenegatives[z]+FalsePositives[z]))/sqrt(round(round(Truepositives[z]+Falsenegatives[z])*round(TrueNegatives[z]+FalsePositives[z])*round(Truepositives[z]+FalsePositives[z])*round(TrueNegatives[z]+Falsenegatives[z])))
762 EER[z]<-.01*(((1-(Sensitivity[z]))*(Truepositives[z]+Falsenegatives[z]))+(Specificity[z]*(1-(Truepositives[z]+Falsenegatives[z]))))
763 }
764 Characterization<-cbind.data.frame(threshold,Truepositives,Falsenegatives,Sensitivity,TrueNegatives,FalsePositives,Specificity,Accuracy,MCC,EER)
765
766 positiveheader<-c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,"RPMS","PMS")
767 positivewithscores<-rbind.data.frame(positiveheader,positivewithscores)
768
769 negativeheader<-c("Substrate","RPMS","PMS")
770 colnames(NegativeWithScores)<-negativeheader
771
772 # write.xlsx(NegativeWithScores,file = FILENAME, sheetName = "Negative Sequences Scored",col.names = TRUE,row.names = FALSE,append = TRUE)
773 # write.xlsx(Characterization,file = FILENAME,sheetName = "Characterization Table",col.names = TRUE,row.names = FALSE,append = TRUE)
774 # write.xlsx(RanksPeptides,file = FILENAME,sheetName = "Ranked Generated Peptides",col.names = FALSE,row.names = FALSE,append = TRUE)
775 # write.xlsx(positivewithscores,file = FILENAME, sheetName = "Positive Sequences Scored",col.names = FALSE,row.names = FALSE,append = TRUE)
776 write.table(x=c("Characterzation Table"),file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")
777 write.table(Characterization,file = FILENAME2, col.names = TRUE,row.names = FALSE, append = TRUE,sep = ",")
778
779
780 write.table(RanksPeptides,file = FILENAME3,append = TRUE,row.names = FALSE,col.names = TRUE,sep = ",")
781
782