1. EventPointer
  2. Commit 50b4241c925533447c2383eb032730da7949f1f4
Browse code

Fixed Coding Style

Juan Pablo Romero authored on 23/10/2018 09:00:38
Showing 18 changed files
.DS_Store
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1 1 
Binary files a/.DS_Store and b/.DS_Store differ
DESCRIPTION
History View file @ 50b4241
... ... 
@@ -2,7 +2,7 @@ Package: EventPointer
2 2 
 Type: Package
3 3 
 Title: An effective identification of alternative splicing events
4 4 
 	   using junction arrays and RNA-Seq data
5 
-Version: 1.5.1
5 
+Version: 1.99.1
6 6 
 Author: Juan Pablo Romero, Juan Ferrer-Bonsoms, Ander Muniategui, Fernando Carazo, Ander Aramburu, Angel Rubio
7 7 
 Maintainer: Juan Pablo Romero <jpromero@ceit.es>
8 8 
 Description: EventPointer is an R package to identify alternative splicing events
... ... 
@@ -54,7 +54,7 @@ Suggests:
54 54 
 License: Artistic-2.0
55 55 
 LazyData: true
56 56 
 RoxygenNote: 6.1.0
57 
-biocViews: AlternativeSplicing, DifferentialSplicing, mRNAMicroarray, RNASeq, Transcription, Sequencing
57 
+biocViews: AlternativeSplicing, DifferentialSplicing, mRNAMicroarray, RNASeq, Transcription, Sequencing, TimeCourse
58 58 
 VignetteBuilder: knitr
59 59 
 Url: https://github.com/jpromeror/EventPointer
60 60 
 BugReports: https://github.com/jpromeror/EventPointer/issues
R/AllEvents_RNASeq_MP.R
History View file @ 50b4241
... ... 
@@ -13,4 +13,4 @@
13 13 
 #' displays the jth splicing event for the ith gene.
14 14 
 #'
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 #' @usage data(AllEvents_RNASeq_MP)
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-NULL
17 16 
\ No newline at end of file
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+NULL
R/AuxFunctions.R
History View file @ 50b4241
... ... 
@@ -1,21 +1,22 @@
1 1 
 #' EventPointer Internal Functions
2 2 
 #'
3 
-#' Internal functions used by EventPointer in the different
3 
+#' Internal functions used by EventPointer in the different
4 4 
 #' steps of the algorithm
5 5 
 #'
6 6 
 #' @keywords internal
7 7 
 #' @name InternalFunctions
8 
-#' @return Internal outputs
9 
-#'
8 
+#' @return Internal outputs
9 
+#'
10 10 
 #'
11 11 
 NULL
12 12
13 13 
 #' @rdname InternalFunctions
14 
-annotateEvents <- function(Events, PSR_Gene, Junc_Gene, Gxx) {
15 
-
14 
+annotateEvents <- function(Events, PSR_Gene,
15 
+    Junc_Gene, Gxx) {
16 16 
     GeneName <- Gxx
17 17 
     ENSGID <- Gxx
18 
-    Chrom <- gsub("chr", "", as.vector(Events[[1]]$P1[1, "Chr"]))
18 
+    Chrom <- gsub("chr", "", as.vector(Events[[1]]$P1[1,
19 
+        "Chr"]))
19 20 
     Result <- vector("list")
20 21 
     Flat <- vector("list")
21 22 
     mm <- 0
... ... 
@@ -31,192 +32,266 @@ annotateEvents <- function(Events, PSR_Gene, Junc_Gene, Gxx) {
31 32 
         PSR_Ref <- c()
32 33 
         Junc_Ref <- c()
33 34
34 
-        ExonsP1 <- which(Events[[ii]]$P1[, "Type"] == "E")
35 
-        JunctionsP1 <- which(Events[[ii]]$P1[, "Type"] == "J")
35 
+        ExonsP1 <- which(Events[[ii]]$P1[,
36 
+            "Type"] == "E")
37 
+        JunctionsP1 <- which(Events[[ii]]$P1[,
38 
+            "Type"] == "J")
36 39
37 40 
         if (length(ExonsP1) > 0) {
38 
-            EPP1 <- Events[[ii]]$P1[ExonsP1, ]
39 
-            PSR_P1 <- sapply(seq_len(nrow(EPP1)), function(x) {
40 
-                which(as.numeric(PSR_Gene[, "Start"]) >= as.numeric(EPP1[x, "Start"]) &
41 
-                as.numeric(PSR_Gene[, "Stop"]) <= as.numeric(EPP1[x, "End"]))
42 
-            })
43 
-            PSR_P1 <- PSR_Gene[unlist(PSR_P1), 1]
44 
-
41 
+            EPP1 <- Events[[ii]]$P1[ExonsP1,
42 
+                ]
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+            PSR_P1 <- sapply(seq_len(nrow(EPP1)),
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+                function(x) {
45 
+                  which(as.numeric(PSR_Gene[,
46 
+                    "Start"]) >= as.numeric(EPP1[x,
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+                    "Start"]) & as.numeric(PSR_Gene[,
48 
+                    "Stop"]) <= as.numeric(EPP1[x,
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+                    "End"]))
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+                })
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+            PSR_P1 <- PSR_Gene[unlist(PSR_P1),
52 
+                1]
45 53 
         }
46 54
47 55 
         if (length(JunctionsP1) > 0) {
48 
-            JPP1 <- Events[[ii]]$P1[JunctionsP1, ]
49 
-            Junc_P1 <- sapply(seq_len(nrow(JPP1)), function(x) {
50 
-                which(as.numeric(Junc_Gene[, "Start"]) == as.numeric(JPP1[x, "Start"]) &
51 
-                  as.numeric(Junc_Gene[, "Stop"]) == as.numeric(JPP1[x, "End"]))
52 
-            })
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-            Junc_P1 <- Junc_Gene[unlist(Junc_P1), 1]
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-        }
55 
-
56 
-
57 
-        ExonsP2 <- which(Events[[ii]]$P2[, "Type"] == "E")
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-        JunctionsP2 <- which(Events[[ii]]$P2[, "Type"] == "J")
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+            JPP1 <- Events[[ii]]$P1[JunctionsP1,
57 
+                ]
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+            Junc_P1 <- sapply(seq_len(nrow(JPP1)),
59 
+                function(x) {
60 
+                  which(as.numeric(Junc_Gene[,
61 
+                    "Start"]) == as.numeric(JPP1[x,
62 
+                    "Start"]) & as.numeric(Junc_Gene[,
63 
+                    "Stop"]) == as.numeric(JPP1[x,
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+                    "End"]))
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+                })
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+            Junc_P1 <- Junc_Gene[unlist(Junc_P1),
67 
+                1]
68 
+        }
69 
+
70 
+
71 
+        ExonsP2 <- which(Events[[ii]]$P2[,
72 
+            "Type"] == "E")
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+        JunctionsP2 <- which(Events[[ii]]$P2[,
74 
+            "Type"] == "J")
59 75
60 76 
         if (length(ExonsP2) > 0) {
61 
-            EPP2 <- Events[[ii]]$P2[ExonsP2, ]
62 
-            PSR_P2 <- sapply(seq_len(nrow(EPP2)), function(x) {
63 
-                which(as.numeric(PSR_Gene[, "Start"]) >= as.numeric(EPP2[x, "Start"]) &
64 
-                  as.numeric(PSR_Gene[, "Stop"]) <= as.numeric(EPP2[x, "End"]))
65 
-            })
66 
-            PSR_P2 <- PSR_Gene[unlist(PSR_P2), 1]
67 
-
77 
+            EPP2 <- Events[[ii]]$P2[ExonsP2,
78 
+                ]
79 
+            PSR_P2 <- sapply(seq_len(nrow(EPP2)),
80 
+                function(x) {
81 
+                  which(as.numeric(PSR_Gene[,
82 
+                    "Start"]) >= as.numeric(EPP2[x,
83 
+                    "Start"]) & as.numeric(PSR_Gene[,
84 
+                    "Stop"]) <= as.numeric(EPP2[x,
85 
+                    "End"]))
86 
+                })
87 
+            PSR_P2 <- PSR_Gene[unlist(PSR_P2),
88 
+                1]
68 89 
         }
69 90
70 91 
         if (length(JunctionsP2) > 0) {
71 
-            JPP2 <- Events[[ii]]$P2[JunctionsP2, ]
72 
-            Junc_P2 <- sapply(seq_len(nrow(JPP2)), function(x) {
73 
-                which(as.numeric(Junc_Gene[, "Start"]) == as.numeric(JPP2[x, "Start"]) &
74 
-                  as.numeric(Junc_Gene[, "Stop"]) == as.numeric(JPP2[x, "End"]))
75 
-            })
76 
-            Junc_P2 <- Junc_Gene[unlist(Junc_P2), 1]
77 
-        }
78 
-
79 
-
80 
-        ExonsRef <- which(Events[[ii]]$Ref[, "Type"] == "E")
81 
-        JunctionsRef <- which(Events[[ii]]$Ref[, "Type"] == "J")
92 
+            JPP2 <- Events[[ii]]$P2[JunctionsP2,
93 
+                ]
94 
+            Junc_P2 <- sapply(seq_len(nrow(JPP2)),
95 
+                function(x) {
96 
+                  which(as.numeric(Junc_Gene[,
97 
+                    "Start"]) == as.numeric(JPP2[x,
98 
+                    "Start"]) & as.numeric(Junc_Gene[,
99 
+                    "Stop"]) == as.numeric(JPP2[x,
100 
+                    "End"]))
101 
+                })
102 
+            Junc_P2 <- Junc_Gene[unlist(Junc_P2),
103 
+                1]
104 
+        }
105 
+
106 
+
107 
+        ExonsRef <- which(Events[[ii]]$Ref[,
108 
+            "Type"] == "E")
109 
+        JunctionsRef <- which(Events[[ii]]$Ref[,
110 
+            "Type"] == "J")
82 111
83 112 
         if (length(ExonsRef) > 0) {
84 
-            EPRef <- Events[[ii]]$Ref[ExonsRef, ]
85 
-            PSR_Ref <- sapply(seq_len(nrow(EPRef)), function(x) {
86 
-                which(as.numeric(PSR_Gene[, "Start"]) >= as.numeric(EPRef[x, "Start"]) &
87 
-                  as.numeric(PSR_Gene[, "Stop"]) <= as.numeric(EPRef[x, "End"]))
88 
-            })
89 
-            PSR_Ref <- PSR_Gene[unlist(PSR_Ref), 1]
90 
-
113 
+            EPRef <- Events[[ii]]$Ref[ExonsRef,
114 
+                ]
115 
+            PSR_Ref <- sapply(seq_len(nrow(EPRef)),
116 
+                function(x) {
117 
+                  which(as.numeric(PSR_Gene[,
118 
+                    "Start"]) >= as.numeric(EPRef[x,
119 
+                    "Start"]) & as.numeric(PSR_Gene[,
120 
+                    "Stop"]) <= as.numeric(EPRef[x,
121 
+                    "End"]))
122 
+                })
123 
+            PSR_Ref <- PSR_Gene[unlist(PSR_Ref),
124 
+                1]
91 125 
         }
92 126
93 127 
         if (length(JunctionsRef) > 0) {
94 
-            JPRef <- Events[[ii]]$Ref[JunctionsRef, ]
95 
-            Junc_Ref <- sapply(seq_len(nrow(JPRef)), function(x) {
96 
-                which(as.numeric(Junc_Gene[, "Start"]) == as.numeric(JPRef[x, "Start"]) &
97 
-                  as.numeric(Junc_Gene[, "Stop"]) == as.numeric(JPRef[x, "End"]))
98 
-            })
99 
-            Junc_Ref <- Junc_Gene[unlist(Junc_Ref), 1]
100 
-        }
101 
-
102 
-
103 
-        # PSR_P2<-sapply(1:nrow(Events[[ii]]$P2),function(x){which(as.numeric(PSR_Gene[,'Start'])>=as.numeric(Events[[ii]]$P2[x,'Start'])
104 
-        # & as.numeric(PSR_Gene[,'Stop'])<=as.numeric(Events[[ii]]$P2[x,'End']))})
105 
-        # PSR_P2<-PSR_Gene[unlist(PSR_P2),6]
106 
-        # Junc_P2<-sapply(1:nrow(Events[[ii]]$P2),function(x){which(as.numeric(Junc_Gene[,'Start'])==as.numeric(Events[[ii]]$P2[x,'Start'])
107 
-        # & as.numeric(Junc_Gene[,'Stop'])==as.numeric(Events[[ii]]$P2[x,'End']))})
108 
-        # Junc_P2<-Junc_Gene[unlist(Junc_P2),1]
109 
-        # PSR_Ref<-sapply(1:nrow(Events[[ii]]$Ref),function(x){which(as.numeric(PSR_Gene[,'Start'])>=as.numeric(Events[[ii]]$Ref[x,'Start'])
110 
-        # & as.numeric(PSR_Gene[,'Stop'])<=as.numeric(Events[[ii]]$Ref[x,'End']))})
111 
-        # PSR_Ref<-PSR_Gene[unlist(PSR_Ref),6]
112 
-        # Junc_Ref<-sapply(1:nrow(Events[[ii]]$Ref),function(x){which(as.numeric(Junc_Gene[,'Start'])==as.numeric(Events[[ii]]$Ref[x,'Start'])
113 
-        # & as.numeric(Junc_Gene[,'Stop'])==as.numeric(Events[[ii]]$Ref[x,'End']))})
114 
-        # Junc_Ref<-Junc_Gene[unlist(Junc_Ref),1]
115 
-
116 
-
117 
-
118 
-
119 
-        Events[[ii]]$Probes_P1 <- c(PSR_P1, Junc_P1)
120 
-        Events[[ii]]$Probes_P2 <- c(PSR_P2, Junc_P2)
121 
-        Events[[ii]]$Probes_Ref <- c(PSR_Ref, Junc_Ref)
122 
-
123 
-        if (length(Events[[ii]]$Probes_P1) > 0 & length(Events[[ii]]$Probes_P2) >
124 
-            0 & length(Events[[ii]]$Probes_Ref) > 0) {
128 
+            JPRef <- Events[[ii]]$Ref[JunctionsRef,
129 
+                ]
130 
+            Junc_Ref <- sapply(seq_len(nrow(JPRef)),
131 
+                function(x) {
132 
+                  which(as.numeric(Junc_Gene[,
133 
+                    "Start"]) == as.numeric(JPRef[x,
134 
+                    "Start"]) & as.numeric(Junc_Gene[,
135 
+                    "Stop"]) == as.numeric(JPRef[x,
136 
+                    "End"]))
137 
+                })
138 
+            Junc_Ref <- Junc_Gene[unlist(Junc_Ref),
139 
+                1]
140 
+        }
141 
+
142 
+
143 
+        Events[[ii]]$Probes_P1 <- c(PSR_P1,
144 
+            Junc_P1)
145 
+        Events[[ii]]$Probes_P2 <- c(PSR_P2,
146 
+            Junc_P2)
147 
+        Events[[ii]]$Probes_Ref <- c(PSR_Ref,
148 
+            Junc_Ref)
149 
+
150 
+        if (length(Events[[ii]]$Probes_P1) >
151 
+            0 & length(Events[[ii]]$Probes_P2) >
152 
+            0 & length(Events[[ii]]$Probes_Ref) >
153 
+            0) {
125 154 
             mm <- mm + 1
126 155
127 156 
             EventNumber <- ii
128 157
129 158 
             EventType <- Events[[ii]]$Type
130 159
131 
-            Positions <- rbind(Events[[ii]]$P1, Events[[ii]]$P2)[, 4:5]
132 
-            Start <- as.numeric(Positions[, 1])
133 
-            End <- as.numeric(Positions[, 2])
134 
-            Start <- Start[which(Start != 0)]
160 
+            Positions <- rbind(Events[[ii]]$P1,
161 
+                Events[[ii]]$P2)[, 4:5]
162 
+            Start <- as.numeric(Positions[,
163 
+                1])
164 
+            End <- as.numeric(Positions[,
165 
+                2])
166 
+            Start <- Start[which(Start !=
167 
+                0)]
135 168 
             End <- End[which(End != 0)]
136 169
137 170 
             # browser()
138 171 
             minGPos <- min(Start)
139 172 
             maxGPos <- max(End)
140 
-            GPos <- paste(Chrom, ":", minGPos, "-", maxGPos, sep = "")
173 
+            GPos <- paste(Chrom, ":", minGPos,
174 
+                "-", maxGPos, sep = "")
141 175
142 
-            CP1s <- which(Events[[ii]]$P1[, 1] == "S")
143 
-            CP1e <- which(Events[[ii]]$P1[, 2] == "E")
176 
+            CP1s <- which(Events[[ii]]$P1[,
177 
+                1] == "S")
178 
+            CP1e <- which(Events[[ii]]$P1[,
179 
+                2] == "E")
144 180
145 
-            if (length(CP1s) > 0 | length(CP1e) > 0) {
181 
+            if (length(CP1s) > 0 | length(CP1e) >
182 
+                0) {
146 183 
                 CC <- c(CP1s, CP1e)
147 
-                Events[[ii]]$P1 <- Events[[ii]]$P1[-CC, ]
184 
+                Events[[ii]]$P1 <- Events[[ii]]$P1[-CC,
185 
+                  ]
148 186 
             }
149 187
150 
-            PS1 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P1[, 1]))
151 
-            PE1 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P1[, 2]))
152 
-            Path1 <- as.matrix(cbind(PS1, PE1))
153 
-            Path1 <- Path1[order(Path1[, 1], Path1[, 2]), , drop = FALSE]
154 
-
155 
-            CP2s <- which(Events[[ii]]$P2[, 1] == "S")
156 
-            CP2e <- which(Events[[ii]]$P2[, 2] == "E")
157 
-
158 
-            if (length(CP2s) > 0 | length(CP2e) > 0) {
188 
+            PS1 <- as.numeric(gsub(".[ab]",
189 
+                "", Events[[ii]]$P1[, 1]))
190 
+            PE1 <- as.numeric(gsub(".[ab]",
191 
+                "", Events[[ii]]$P1[, 2]))
192 
+            Path1 <- as.matrix(cbind(PS1,
193 
+                PE1))
194 
+            Path1 <- Path1[order(Path1[,
195 
+                1], Path1[, 2]), , drop = FALSE]
196 
+
197 
+            CP2s <- which(Events[[ii]]$P2[,
198 
+                1] == "S")
199 
+            CP2e <- which(Events[[ii]]$P2[,
200 
+                2] == "E")
201 
+
202 
+            if (length(CP2s) > 0 | length(CP2e) >
203 
+                0) {
159 204 
                 CC <- c(CP2s, CP2e)
160 
-                Events[[ii]]$P2 <- Events[[ii]]$P2[-CC, ]
205 
+                Events[[ii]]$P2 <- Events[[ii]]$P2[-CC,
206 
+                  ]
161 207 
             }
162 208
163 
-            PS2 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P2[, 1]))
164 
-            PE2 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P2[, 2]))
165 
-            Path2 <- as.matrix(cbind(PS2, PE2))
166 
-            Path2 <- Path2[order(Path2[, 1], Path2[, 2]), , drop = FALSE]
167 
-
168 
-            CPRs <- which(Events[[ii]]$Ref[, 1] == "S")
169 
-            CPRe <- which(Events[[ii]]$Ref[, 2] == "E")
170 
-
171 
-            if (length(CPRs) > 0 | length(CPRe) > 0) {
209 
+            PS2 <- as.numeric(gsub(".[ab]",
210 
+                "", Events[[ii]]$P2[, 1]))
211 
+            PE2 <- as.numeric(gsub(".[ab]",
212 
+                "", Events[[ii]]$P2[, 2]))
213 
+            Path2 <- as.matrix(cbind(PS2,
214 
+                PE2))
215 
+            Path2 <- Path2[order(Path2[,
216 
+                1], Path2[, 2]), , drop = FALSE]
217 
+
218 
+            CPRs <- which(Events[[ii]]$Ref[,
219 
+                1] == "S")
220 
+            CPRe <- which(Events[[ii]]$Ref[,
221 
+                2] == "E")
222 
+
223 
+            if (length(CPRs) > 0 | length(CPRe) >
224 
+                0) {
172 225 
                 CC <- c(CPRs, CPRe)
173 
-                Events[[ii]]$Ref <- Events[[ii]]$Ref[-CC, ]
226 
+                Events[[ii]]$Ref <- Events[[ii]]$Ref[-CC,
227 
+                  ]
174 228 
             }
175 229
176 
-            PSR <- as.numeric(gsub(".[ab]", "", Events[[ii]]$Ref[, 1]))
177 
-            PER <- as.numeric(gsub(".[ab]", "", Events[[ii]]$Ref[, 2]))
178 
-            PathR <- as.matrix(cbind(PSR, PER))
179 
-            PathR <- PathR[order(PathR[, 1], PathR[, 2]), , drop = FALSE]
180 
-
181 
-
182 
-            Path1 <- paste(Path1[, 1], "-", Path1[, 2], sep = "", collapse = ",")
183 
-            Path2 <- paste(Path2[, 1], "-", Path2[, 2], sep = "", collapse = ",")
184 
-            PathR <- paste(PathR[, 1], "-", PathR[, 2], sep = "", collapse = ",")
185 
-
186 
-            ProbesP1 <- paste(Events[[ii]]$Probes_P1, collapse = ",")
187 
-            ProbesP2 <- paste(Events[[ii]]$Probes_P2, collapse = ",")
188 
-            ProbesR <- paste(Events[[ii]]$Probes_Ref, collapse = ",")
189 
-
190 
-            NEv <- data.frame(GeneName, ENSGID, EventNumber, EventType, GPos, Path1,
191 
-                Path2, PathR, ProbesP1, ProbesP2, ProbesR, stringsAsFactors = FALSE)
230 
+            PSR <- as.numeric(gsub(".[ab]",
231 
+                "", Events[[ii]]$Ref[, 1]))
232 
+            PER <- as.numeric(gsub(".[ab]",
233 
+                "", Events[[ii]]$Ref[, 2]))
234 
+            PathR <- as.matrix(cbind(PSR,
235 
+                PER))
236 
+            PathR <- PathR[order(PathR[,
237 
+                1], PathR[, 2]), , drop = FALSE]
238 
+
239 
+
240 
+            Path1 <- paste(Path1[, 1], "-",
241 
+                Path1[, 2], sep = "", collapse = ",")
242 
+            Path2 <- paste(Path2[, 1], "-",
243 
+                Path2[, 2], sep = "", collapse = ",")
244 
+            PathR <- paste(PathR[, 1], "-",
245 
+                PathR[, 2], sep = "", collapse = ",")
246 
+
247 
+            ProbesP1 <- paste(Events[[ii]]$Probes_P1,
248 
+                collapse = ",")
249 
+            ProbesP2 <- paste(Events[[ii]]$Probes_P2,
250 
+                collapse = ",")
251 
+            ProbesR <- paste(Events[[ii]]$Probes_Ref,
252 
+                collapse = ",")
253 
+
254 
+            NEv <- data.frame(GeneName, ENSGID,
255 
+                EventNumber, EventType, GPos,
256 
+                Path1, Path2, PathR, ProbesP1,
257 
+                ProbesP2, ProbesR, stringsAsFactors = FALSE)
192 258 
             Result[[mm]] <- NEv
193 259
194 260
195 261 
             Tprobes <- rbind(PSR_Gene, Junc_Gene)
196 
-            ii.P1 <- match(Events[[ii]]$Probes_P1, Tprobes[, 1])
197 
-            ii.P2 <- match(Events[[ii]]$Probes_P2, Tprobes[, 1])
198 
-            ii.R <- match(Events[[ii]]$Probes_Ref, Tprobes[, 1])
262 
+            ii.P1 <- match(Events[[ii]]$Probes_P1,
263 
+                Tprobes[, 1])
264 
+            ii.P2 <- match(Events[[ii]]$Probes_P2,
265 
+                Tprobes[, 1])
266 
+            ii.R <- match(Events[[ii]]$Probes_Ref,
267 
+                Tprobes[, 1])
199 268
200 269 
             lP1 <- length(ii.P1)
201 270 
             lP2 <- length(ii.P2)
202 271 
             lRef <- length(ii.R)
203 272
204 
-            xRef <- rep(paste(GeneName, "_", EventNumber, "_Ref", sep = ""), lRef)
205 
-            xP1 <- rep(paste(GeneName, "_", EventNumber, "_P1", sep = ""), lP1)
206 
-            xP2 <- rep(paste(GeneName, "_", EventNumber, "_P2", sep = ""), lP2)
207 
-            xTot <- rep(paste(GeneName, "_", EventNumber, sep = ""), lP1 + lP2 +
273 
+            xRef <- rep(paste(GeneName, "_",
274 
+                EventNumber, "_Ref", sep = ""),
208 275 
                 lRef)
209 
-
210 
-            AllProbes <- c(Events[[ii]]$Probes_Ref, Events[[ii]]$Probes_P1, Events[[ii]]$Probes_P2)
211 
-            flat_gene <- cbind(AllProbes, Tprobes[c(ii.R, ii.P1, ii.P2), c(2, 3,
212 
-                9)], c(xRef, xP1, xP2), xTot)
276 
+            xP1 <- rep(paste(GeneName, "_",
277 
+                EventNumber, "_P1", sep = ""),
278 
+                lP1)
279 
+            xP2 <- rep(paste(GeneName, "_",
280 
+                EventNumber, "_P2", sep = ""),
281 
+                lP2)
282 
+            xTot <- rep(paste(GeneName, "_",
283 
+                EventNumber, sep = ""), lP1 +
284 
+                lP2 + lRef)
285 
+
286 
+            AllProbes <- c(Events[[ii]]$Probes_Ref,
287 
+                Events[[ii]]$Probes_P1, Events[[ii]]$Probes_P2)
288 
+            flat_gene <- cbind(AllProbes,
289 
+                Tprobes[c(ii.R, ii.P1, ii.P2),
290 
+                  c(2, 3, 9)], c(xRef, xP1,
291 
+                  xP2), xTot)
213 292
214 293 
             Flat[[mm]] <- flat_gene
215 
-
216 
-
217 
-
218 294 
         }
219 
-
220 295 
     }
221 296
222 297 
     Result <- do.call(rbind, Result)
... ... 
@@ -226,22 +301,26 @@ annotateEvents <- function(Events, PSR_Gene, Junc_Gene, Gxx) {
226 301
227 302
228 303 
 #' @rdname InternalFunctions
229 
-annotateEventsMultipath <- function(Events, PSR_Gene, Junc_Gene, Gxx, paths) {
304 
+annotateEventsMultipath <- function(Events,
305 
+    PSR_Gene, Junc_Gene, Gxx, paths) {
230 306 
     GeneName <- Gxx
231 307 
     ENSGID <- Gxx
232 
-    Chrom <- gsub("chr", "", as.vector(Events[[1]]$P1[1, "Chr"]))
308 
+    Chrom <- gsub("chr", "", as.vector(Events[[1]]$P1[1,
309 
+        "Chr"]))
233 310 
     Result <- vector("list")
234 311 
     Flat <- vector("list")
235 312 
     mm <- 0
236 313
237 314 
     for (ii in seq_along(Events)) {
238 
-
239 315 
         for (kk in seq_len(paths)) {
240 
-            command <- paste0("Events[[ii]]$Probes_P", kk, "<-NULL")
316 
+            command <- paste0("Events[[ii]]$Probes_P",
317 
+                kk, "<-NULL")
241 318 
             eval(parse(text = command))
242 
-            command <- paste0("PSR_P", kk, "<-c()")
319 
+            command <- paste0("PSR_P", kk,
320 
+                "<-c()")
243 321 
             eval(parse(text = command))
244 
-            command <- paste0("Junc_P", kk, "<-c()")
322 
+            command <- paste0("Junc_P", kk,
323 
+                "<-c()")
245 324 
             eval(parse(text = command))
246 325 
         }
247 326 
         Events[[ii]]$Probes_Ref <- NULL
... ... 
@@ -250,85 +329,121 @@ annotateEventsMultipath <- function(Events, PSR_Gene, Junc_Gene, Gxx, paths) {
250 329
251 330
252 331 
         for (kk in seq_len(paths)) {
253 
-
254 
-            command <- paste0("ExonsP", kk, "<-which(Events[[ii]]$P", kk, "[,'Type']=='E')")
332 
+            command <- paste0("ExonsP", kk,
333 
+                "<-which(Events[[ii]]$P",
334 
+                kk, "[,'Type']=='E')")
255 335 
             eval(parse(text = command))
256 336
257 
-            command <- paste0("JunctionsP", kk, "<-which(Events[[ii]]$P", kk, "[,'Type']=='J')")
337 
+            command <- paste0("JunctionsP",
338 
+                kk, "<-which(Events[[ii]]$P",
339 
+                kk, "[,'Type']=='J')")
258 340 
             eval(parse(text = command))
259 341
260 342 
             # ExonsP1,2,3 and JunctionP1,2,... etc
261 343
262 
-            command <- paste0("a <- length(ExonsP", kk, ">0)")
344 
+            command <- paste0("a <- length(ExonsP",
345 
+                kk, ">0)")
263 346 
             eval(parse(text = command))
264 347 
             if (a > 0) {
265 
-                command <- paste0("EPP", kk, "<-Events[[ii]]$P", kk, "[ExonsP", kk,
266 
-                  ",]")
348 
+                command <- paste0("EPP",
349 
+                  kk, "<-Events[[ii]]$P",
350 
+                  kk, "[ExonsP", kk, ",]")
267 351 
                 eval(parse(text = command))
268 
-                command <- paste0("PSR_P", kk, "<-sapply(1:nrow(EPP", kk, "),function(x){which(as.numeric(PSR_Gene[,'Start'])>=as.numeric(EPP",
352 
+                command <- paste0("PSR_P",
353 
+                  kk, "<-sapply(1:nrow(EPP",
354 
+                  kk, "),function(x){which(as.numeric(PSR_Gene[,'Start'])>=as.numeric(EPP",
269 355 
                   kk, "[x,'Start']) & as.numeric(PSR_Gene[,'Stop'])<=as.numeric(EPP",
270 356 
                   kk, "[x,'End']))})")
271 357 
                 eval(parse(text = command))
272 
-                command <- paste0("PSR_P", kk, "<-PSR_Gene[unlist(PSR_P", kk, "),1]")
358 
+                command <- paste0("PSR_P",
359 
+                  kk, "<-PSR_Gene[unlist(PSR_P",
360 
+                  kk, "),1]")
273 361 
                 eval(parse(text = command))
274 362 
             }
275 363
276 
-            command <- paste0("a <- length(JunctionsP", kk, ">0)")
364 
+            command <- paste0("a <- length(JunctionsP",
365 
+                kk, ">0)")
277 366 
             eval(parse(text = command))
278 367 
             if (a > 0) {
279 
-                command <- paste0("JPP", kk, "<-Events[[ii]]$P", kk, "[JunctionsP",
280 
-                  kk, ",]")
368 
+                command <- paste0("JPP",
369 
+                  kk, "<-Events[[ii]]$P",
370 
+                  kk, "[JunctionsP", kk,
371 
+                  ",]")
281 372 
                 eval(parse(text = command))
282 
-                command <- paste0("Junc_P", kk, "<-sapply(1:nrow(JPP", kk, "),function(x){which(as.numeric(Junc_Gene[,'Start'])==as.numeric(JPP",
373 
+                command <- paste0("Junc_P",
374 
+                  kk, "<-sapply(1:nrow(JPP",
375 
+                  kk, "),function(x){which(as.numeric(Junc_Gene[,'Start'])==as.numeric(JPP",
283 376 
                   kk, "[x,'Start']) & as.numeric(Junc_Gene[,'Stop'])==as.numeric(JPP",
284 377 
                   kk, "[x,'End']))})")
285 378 
                 eval(parse(text = command))
286 
-                command <- paste0("Junc_P", kk, "<-Junc_Gene[unlist(Junc_P", kk,
287 
-                  "),1]")
379 
+                command <- paste0("Junc_P",
380 
+                  kk, "<-Junc_Gene[unlist(Junc_P",
381 
+                  kk, "),1]")
288 382 
                 eval(parse(text = command))
289 383 
             }
290 384 
         }
291 385
292 
-        ExonsRef <- which(Events[[ii]]$Ref[, "Type"] == "E")
293 
-        JunctionsRef <- which(Events[[ii]]$Ref[, "Type"] == "J")
386 
+        ExonsRef <- which(Events[[ii]]$Ref[,
387 
+            "Type"] == "E")
388 
+        JunctionsRef <- which(Events[[ii]]$Ref[,
389 
+            "Type"] == "J")
294 390
295 391 
         if (length(ExonsRef) > 0) {
296 
-            EPRef <- Events[[ii]]$Ref[ExonsRef, ]
297 
-            PSR_Ref <- sapply(seq_len(nrow(EPRef)), function(x) {
298 
-                which(as.numeric(PSR_Gene[, "Start"]) >= as.numeric(EPRef[x, "Start"]) &
299 
-                  as.numeric(PSR_Gene[, "Stop"]) <= as.numeric(EPRef[x, "End"]))
300 
-            })
301 
-            PSR_Ref <- PSR_Gene[unlist(PSR_Ref), 1]
302 
-
392 
+            EPRef <- Events[[ii]]$Ref[ExonsRef,
393 
+                ]
394 
+            PSR_Ref <- sapply(seq_len(nrow(EPRef)),
395 
+                function(x) {
396 
+                  which(as.numeric(PSR_Gene[,
397 
+                    "Start"]) >= as.numeric(EPRef[x,
398 
+                    "Start"]) & as.numeric(PSR_Gene[,
399 
+                    "Stop"]) <= as.numeric(EPRef[x,
400 
+                    "End"]))
401 
+                })
402 
+            PSR_Ref <- PSR_Gene[unlist(PSR_Ref),
403 
+                1]
303 404 
         }
304 405
305 406 
         if (length(JunctionsRef) > 0) {
306 
-            JPRef <- Events[[ii]]$Ref[JunctionsRef, ]
307 
-            Junc_Ref <- sapply(seq_len(nrow(JPRef)), function(x) {
308 
-                which(as.numeric(Junc_Gene[, "Start"]) == as.numeric(JPRef[x, "Start"]) &
309 
-                  as.numeric(Junc_Gene[, "Stop"]) == as.numeric(JPRef[x, "End"]))
310 
-            })
311 
-            Junc_Ref <- Junc_Gene[unlist(Junc_Ref), 1]
407 
+            JPRef <- Events[[ii]]$Ref[JunctionsRef,
408 
+                ]
409 
+            Junc_Ref <- sapply(seq_len(nrow(JPRef)),
410 
+                function(x) {
411 
+                  which(as.numeric(Junc_Gene[,
412 
+                    "Start"]) == as.numeric(JPRef[x,
413 
+                    "Start"]) & as.numeric(Junc_Gene[,
414 
+                    "Stop"]) == as.numeric(JPRef[x,
415 
+                    "End"]))
416 
+                })
417 
+            Junc_Ref <- Junc_Gene[unlist(Junc_Ref),
418 
+                1]
312 419 
         }
313 420
314 421
315 422 
         for (kk in seq_len(paths)) {
316 
-            command <- paste0("Events[[ii]]$Probes_P", kk, "<-c(PSR_P", kk, ",Junc_P",
423 
+            command <- paste0("Events[[ii]]$Probes_P",
424 
+                kk, "<-c(PSR_P", kk, ",Junc_P",
317 425 
                 kk, ")")
318 426 
             eval(parse(text = command))
319 427 
         }
320 
-        Events[[ii]]$Probes_Ref <- c(PSR_Ref, Junc_Ref)
428 
+        Events[[ii]]$Probes_Ref <- c(PSR_Ref,
429 
+            Junc_Ref)
321 430
322 431
323 
-        # only the events in which all their events are able to be measured are shown. It
324 
-        # is necesary to know the number of paths of each Event
325 
-        for (kk in seq_len((Events[[ii]]$NumP + 1))) {
432 
+        # only the events in which all their
433 
+        # events are able to be measured are
434 
+        # shown. It is necesary to know the
435 
+        # number of paths of each Event
436 
+        for (kk in seq_len((Events[[ii]]$NumP +
437 
+            1))) {
326 438 
             if (kk == 1) {
327 
-                a <- paste0("a <- length(Events[[ii]]$Probes_P", kk, ")>0 & ")
328 
-            } else if (kk == (Events[[ii]]$NumP + 1)) {
439 
+                a <- paste0("a <- length(Events[[ii]]$Probes_P",
440 
+                  kk, ")>0 & ")
441 
+            } else if (kk == (Events[[ii]]$NumP +
442 
+                1)) {
329 443 
                 a <- paste0(a, "length(Events[[ii]]$Probes_Ref)>0")
330 444 
             } else {
331 
-                a <- paste0(a, "length(Events[[ii]]$Probes_P", kk, ")>0 & ")
445 
+                a <- paste0(a, "length(Events[[ii]]$Probes_P",
446 
+                  kk, ")>0 & ")
332 447 
             }
333 448 
         }
334 449 
         eval(parse(text = a))
... ... 
@@ -346,93 +461,131 @@ annotateEventsMultipath <- function(Events, PSR_Gene, Junc_Gene, Gxx, paths) {
346 461 
             EventNumP <- Events[[ii]]$NumP
347 462 
             for (kk in seq_len(EventNumP)) {
348 463 
                 if (kk == 1) {
349 
-                  Positions <- paste0("Positions <- rbind(Events[[ii]]$P", kk)
464 
+                  Positions <- paste0("Positions <- rbind(Events[[ii]]$P",
465 
+                    kk)
350 466 
                 } else if (kk == EventNumP) {
351 
-                  Positions <- paste0(Positions, ",Events[[ii]]$P", kk, ")[,4:5]")
467 
+                  Positions <- paste0(Positions,
468 
+                    ",Events[[ii]]$P", kk,
469 
+                    ")[,4:5]")
352 470 
                 } else {
353 
-                  Positions <- paste0(Positions, ",Events[[ii]]$P", kk)
471 
+                  Positions <- paste0(Positions,
472 
+                    ",Events[[ii]]$P", kk)
354 473 
                 }
355 474 
             }
356 475 
             eval(parse(text = Positions))
357 476 
             # Positions<-rbind(Events[[ii]]$P1,Events[[ii]]$P2)[,4:5]
358 
-            Start <- as.numeric(Positions[, 1])
359 
-            End <- as.numeric(Positions[, 2])
360 
-            Start <- Start[which(Start != 0)]
477 
+            Start <- as.numeric(Positions[,
478 
+                1])
479 
+            End <- as.numeric(Positions[,
480 
+                2])
481 
+            Start <- Start[which(Start !=
482 
+                0)]
361 483 
             End <- End[which(End != 0)]
362 484
363 485 
             # browser()
364 486 
             minGPos <- min(Start)
365 487 
             maxGPos <- max(End)
366 
-            GPos <- paste(Chrom, ":", minGPos, "-", maxGPos, sep = "")
488 
+            GPos <- paste(Chrom, ":", minGPos,
489 
+                "-", maxGPos, sep = "")
367 490
368 491 
             for (kk in seq_len(EventNumP)) {
369 
-                command <- paste0("CP", kk, "s<-which(Events[[ii]]$P", kk, "[,1]=='S')")
492 
+                command <- paste0("CP", kk,
493 
+                  "s<-which(Events[[ii]]$P",
494 
+                  kk, "[,1]=='S')")
370 495 
                 eval(parse(text = command))
371 
-                command <- paste0("CP", kk, "e<-which(Events[[ii]]$P", kk, "[,2]=='E')")
496 
+                command <- paste0("CP", kk,
497 
+                  "e<-which(Events[[ii]]$P",
498 
+                  kk, "[,2]=='E')")
372 499 
                 eval(parse(text = command))
373 
-                a <- paste0("a<-length(CP", kk, "s)>0|length(CP", kk, "e)>0")
500 
+                a <- paste0("a<-length(CP",
501 
+                  kk, "s)>0|length(CP", kk,
502 
+                  "e)>0")
374 503 
                 eval(parse(text = a))
375 504 
                 if (a) {
376 
-                  command <- paste0("CC<-c(CP", kk, "s,CP", kk, "e)")
505 
+                  command <- paste0("CC<-c(CP",
506 
+                    kk, "s,CP", kk, "e)")
377 507 
                   eval(parse(text = command))
378 
-                  command <- paste0("Events[[ii]]$P", kk, "<-Events[[ii]]$P", kk,
379 
-                    "[-CC,]")
508 
+                  command <- paste0("Events[[ii]]$P",
509 
+                    kk, "<-Events[[ii]]$P",
510 
+                    kk, "[-CC,]")
380 511 
                   eval(parse(text = command))
381 512 
                 }
382 
-                command <- paste0("PS", kk, "<-as.numeric(gsub('.[ab]','',Events[[ii]]$P",
513 
+                command <- paste0("PS", kk,
514 
+                  "<-as.numeric(gsub('.[ab]','',Events[[ii]]$P",
383 515 
                   kk, "[,1]))")
384 516 
                 eval(parse(text = command))
385 
-                command <- paste0("PE", kk, "<-as.numeric(gsub('.[ab]','',Events[[ii]]$P",
517 
+                command <- paste0("PE", kk,
518 
+                  "<-as.numeric(gsub('.[ab]','',Events[[ii]]$P",
386 519 
                   kk, "[,2]))")
387 520 
                 eval(parse(text = command))
388 
-                command <- paste0("Path", kk, "<-as.matrix(cbind(PS", kk, ",PE",
389 
-                  kk, "))")
521 
+                command <- paste0("Path",
522 
+                  kk, "<-as.matrix(cbind(PS",
523 
+                  kk, ",PE", kk, "))")
390 524 
                 eval(parse(text = command))
391 
-                command <- paste0("Path", kk, "<-Path", kk, "[order(Path", kk, "[,1],Path",
392 
-                  kk, "[,2]),,drop=FALSE]")
525 
+                command <- paste0("Path",
526 
+                  kk, "<-Path", kk, "[order(Path",
527 
+                  kk, "[,1],Path", kk, "[,2]),,drop=FALSE]")
393 528 
                 eval(parse(text = command))
394 529 
             }
395 530
396 531
397 
-            CPRs <- which(Events[[ii]]$Ref[, 1] == "S")
398 
-            CPRe <- which(Events[[ii]]$Ref[, 2] == "E")
532 
+            CPRs <- which(Events[[ii]]$Ref[,
533 
+                1] == "S")
534 
+            CPRe <- which(Events[[ii]]$Ref[,
535 
+                2] == "E")
399 536
400 
-            if (length(CPRs) > 0 | length(CPRe) > 0) {
537 
+            if (length(CPRs) > 0 | length(CPRe) >
538 
+                0) {
401 539 
                 CC <- c(CPRs, CPRe)
402 
-                Events[[ii]]$Ref <- Events[[ii]]$Ref[-CC, ]
540 
+                Events[[ii]]$Ref <- Events[[ii]]$Ref[-CC,
541 
+                  ]
403 542 
             }
404 543
405 
-            PSR <- as.numeric(gsub(".[ab]", "", Events[[ii]]$Ref[, 1]))
406 
-            PER <- as.numeric(gsub(".[ab]", "", Events[[ii]]$Ref[, 2]))
407 
-            PathR <- as.matrix(cbind(PSR, PER))
408 
-            PathR <- PathR[order(PathR[, 1], PathR[, 2]), , drop = FALSE]
409 
-
410 
-            PathR <- paste(PathR[, 1], "-", PathR[, 2], sep = "", collapse = ",")
411 
-            ProbesR <- paste(Events[[ii]]$Probes_Ref, collapse = ",")
544 
+            PSR <- as.numeric(gsub(".[ab]",
545 
+                "", Events[[ii]]$Ref[, 1]))
546 
+            PER <- as.numeric(gsub(".[ab]",
547 
+                "", Events[[ii]]$Ref[, 2]))
548 
+            PathR <- as.matrix(cbind(PSR,
549 
+                PER))
550 
+            PathR <- PathR[order(PathR[,
551 
+                1], PathR[, 2]), , drop = FALSE]
552 
+
553 
+            PathR <- paste(PathR[, 1], "-",
554 
+                PathR[, 2], sep = "", collapse = ",")
555 
+            ProbesR <- paste(Events[[ii]]$Probes_Ref,
556 
+                collapse = ",")
412 557 
             NEv <- "NEv<-data.frame(GeneName,ENSGID,EventNumber,EventType,GPos,EventNumP,"
413 558 
             for (kk in seq_len(paths)) {
414 559 
                 if (kk <= EventNumP) {
415 
-                  command <- paste0("Path", kk, "<-paste(Path", kk, "[,1],'-',Path",
416 
-                    kk, "[,2],sep='',collapse=',')")
560 
+                  command <- paste0("Path",
561 
+                    kk, "<-paste(Path", kk,
562 
+                    "[,1],'-',Path", kk,
563 
+                    "[,2],sep='',collapse=',')")
417 564 
                   eval(parse(text = command))
418 
-                  command <- paste0("ProbesP", kk, "<-paste(Events[[ii]]$Probes_P",
565 
+                  command <- paste0("ProbesP",
566 
+                    kk, "<-paste(Events[[ii]]$Probes_P",
419 567 
                     kk, ",collapse=',')")
420 568 
                   eval(parse(text = command))
421 569 
                 } else {
422 
-                  command <- paste0("Path", kk, "<-'-'")
570 
+                  command <- paste0("Path",
571 
+                    kk, "<-'-'")
423 572 
                   eval(parse(text = command))
424 
-                  command <- paste0("ProbesP", kk, "<-'-'")
573 
+                  command <- paste0("ProbesP",
574 
+                    kk, "<-'-'")
425 575 
                   eval(parse(text = command))
426 576 
                 }
427 
-                NEv <- paste0(NEv, "Path", kk, ",")
577 
+                NEv <- paste0(NEv, "Path",
578 
+                  kk, ",")
428 579 
             }
429 580 
             NEv <- paste0(NEv, "PathR,")
430 581 
             for (kk in seq_len(paths)) {
431 
-                NEv <- paste0(NEv, "ProbesP", kk, ",")
582 
+                NEv <- paste0(NEv, "ProbesP",
583 
+                  kk, ",")
432 584 
             }
433 585 
             NEv <- paste0(NEv, "ProbesR,stringsAsFactors = FALSE)")
434 586 
             eval(parse(text = NEv))
435 
-            # NEv<-data.frame(GeneName,ENSGID,EventNumber,EventType,GPos,Path1,Path2,PathR,ProbesP1,ProbesP2,ProbesR,stringsAsFactors
587 
+            # NEv<-data.frame(GeneName,ENSGID,EventNumber,EventType,GPos,
588 
+            # Path1,Path2,PathR,ProbesP1,ProbesP2,ProbesR,stringsAsFactors
436 589 
             # = FALSE)
437 590 
             Result[[mm]] <- NEv
438 591
... ... 
@@ -442,50 +595,64 @@ annotateEventsMultipath <- function(Events, PSR_Gene, Junc_Gene, Gxx, paths) {
442 595 
             AllProbes <- "AllProbes<-c(Events[[ii]]$Probes_Ref,"
443 596 
             flat_gene <- "flat_gene<-cbind(AllProbes,Tprobes[c(ii.R,"
444 597 
             for (kk in seq_len(EventNumP)) {
445 
-                command <- paste0("ii.P", kk, "<-match(Events[[ii]]$Probes_P", kk,
446 
-                  ",Tprobes[,1])")
598 
+                command <- paste0("ii.P",
599 
+                  kk, "<-match(Events[[ii]]$Probes_P",
600 
+                  kk, ",Tprobes[,1])")
447 601 
                 eval(parse(text = command))
448 
-                command <- paste0("lP", kk, "<-length(ii.P", kk, ")")
602 
+                command <- paste0("lP", kk,
603 
+                  "<-length(ii.P", kk, ")")
449 604 
                 eval(parse(text = command))
450 
-                command <- paste0("xP", kk, "<-rep(paste(GeneName,'_',EventNumber,'_P",
451 
-                  kk, "',sep=''),lP", kk, ")")
605 
+                command <- paste0("xP", kk,
606 
+                  "<-rep(paste(GeneName,'_',EventNumber,'_P",
607 
+                  kk, "',sep=''),lP", kk,
608 
+                  ")")
452 609 
                 eval(parse(text = command))
453 
-                xTot <- paste0(xTot, "lP", kk, "+")
610 
+                xTot <- paste0(xTot, "lP",
611 
+                  kk, "+")
454 612 
                 if (kk == EventNumP) {
455 
-                  AllProbes <- paste0(AllProbes, "Events[[ii]]$Probes_P", kk, ")")
456 
-                  flat_gene <- paste0(flat_gene, "ii.P", kk, "),c(2,3,9)],c(xRef,")
613 
+                  AllProbes <- paste0(AllProbes,
614 
+                    "Events[[ii]]$Probes_P",
615 
+                    kk, ")")
616 
+                  flat_gene <- paste0(flat_gene,
617 
+                    "ii.P", kk, "),c(2,3,9)],c(xRef,")
457 618 
                   for (zz in seq_len(EventNumP)) {
458 619 
                     if (zz == EventNumP) {
459 
-                      flat_gene <- paste0(flat_gene, "xP", zz, "),xTot)")
620 
+                      flat_gene <- paste0(flat_gene,
621 
+                        "xP", zz, "),xTot)")
460 622 
                     } else {
461 
-                      flat_gene <- paste0(flat_gene, "xP", zz, ",")
623 
+                      flat_gene <- paste0(flat_gene,
624 
+                        "xP", zz, ",")
462 625 
                     }
463 
-
464 626 
                   }
465 627 
                 } else {
466 
-                  AllProbes <- paste0(AllProbes, "Events[[ii]]$Probes_P", kk, ",")
467 
-                  flat_gene <- paste0(flat_gene, "ii.P", kk, ",")
628 
+                  AllProbes <- paste0(AllProbes,
629 
+                    "Events[[ii]]$Probes_P",
630 
+                    kk, ",")
631 
+                  flat_gene <- paste0(flat_gene,
632 
+                    "ii.P", kk, ",")
468 633 
                 }
469 634 
             }
470 635 
             xTot <- paste0(xTot, "lRef)")
471 636
472 
-            ii.R <- match(Events[[ii]]$Probes_Ref, Tprobes[, 1])
637 
+            ii.R <- match(Events[[ii]]$Probes_Ref,
638 
+                Tprobes[, 1])
473 639 
             lRef <- length(ii.R)
474 
-            xRef <- rep(paste(GeneName, "_", EventNumber, "_Ref", sep = ""), lRef)
640 
+            xRef <- rep(paste(GeneName, "_",
641 
+                EventNumber, "_Ref", sep = ""),
642 
+                lRef)
475 643
476 644 
             eval(parse(text = xTot))
477 645 
             eval(parse(text = AllProbes))
478 646 
             eval(parse(text = flat_gene))
479 
-            # AllProbes<-c(Events[[ii]]$Probes_Ref,Events[[ii]]$Probes_P1,Events[[ii]]$Probes_P2)
480 
-            # flat_gene<-cbind(AllProbes,Tprobes[c(ii.R,ii.P1,ii.P2),c(2,3,9)],c(xRef,xP1,xP2),xTot)
481 
-            colnames(flat_gene) <- c("Probe_ID", "X", "Y", "Probe_Sequence", "Group_ID",
482 
-                "Unit_ID")
647 
+            # AllProbes<-c(Events[[ii]]$Probes_Ref,Events[[ii]]$Probes_P1,
648 
+            # Events[[ii]]$Probes_P2)
649 
+            # flat_gene<-cbind(AllProbes,Tprobes[c(ii.R,ii.P1,ii.P2),c(2,3,9)],
650 
+            # c(xRef,xP1,xP2),xTot)
651 
+            colnames(flat_gene) <- c("Probe_ID",
652 
+                "X", "Y", "Probe_Sequence",
653 
+                "Group_ID", "Unit_ID")
483 654 
             Flat[[mm]] <- flat_gene
484 
-
485 
-
486 
-
487 655 
         }
488 
-
489 656 
     }
490 657
491 658 
     Result <- do.call(rbind, Result)
... ... 
@@ -498,15 +665,16 @@ annotateEventsMultipath <- function(Events, PSR_Gene, Junc_Gene, Gxx, paths) {
498 665 
 AnnotateEvents_RNASeq <- function(Events) {
499 666 
     Result <- vector("list", length = length(Events))
500 667 
     for (ii in seq_along(Events)) {
501 
-
502 
-
503 668 
         GeneName <- as.vector(Events[[ii]]$GeneName)
504 669 
         GeneID <- as.vector(Events[[ii]]$Gene)
505 670 
         EventNumber <- ii
506 
-        EventID <- paste(GeneID, "_", EventNumber, sep = "")
671 
+        EventID <- paste(GeneID, "_", EventNumber,
672 
+            sep = "")
507 673 
         EventType <- Events[[ii]]$Type
508 
-        Chrom <- as.vector(Events[[ii]]$P1[1, "Chr"])
509 
-        Positions <- rbind(Events[[ii]]$P1, Events[[ii]]$P2)[, 4:5]
674 
+        Chrom <- as.vector(Events[[ii]]$P1[1,
675 
+            "Chr"])
676 
+        Positions <- rbind(Events[[ii]]$P1,
677 
+            Events[[ii]]$P2)[, 4:5]
510 678 
         Start <- as.numeric(Positions[, 1])
511 679 
         End <- as.numeric(Positions[, 2])
512 680 
         Start <- Start[which(Start != 0)]
... ... 
@@ -515,87 +683,115 @@ AnnotateEvents_RNASeq <- function(Events) {
515 683 
         # browser()
516 684 
         minGPos <- min(Start)
517 685 
         maxGPos <- max(End)
518 
-        GPos <- paste(Chrom, ":", minGPos, "-", maxGPos, sep = "")
686 
+        GPos <- paste(Chrom, ":", minGPos,
687 
+            "-", maxGPos, sep = "")
519 688
520 
-        CP1s <- which(Events[[ii]]$P1[, 1] == "S")
521 
-        CP1e <- which(Events[[ii]]$P1[, 2] == "E")
689 
+        CP1s <- which(Events[[ii]]$P1[, 1] ==
690 
+            "S")
691 
+        CP1e <- which(Events[[ii]]$P1[, 2] ==
692 
+            "E")
522 693
523 
-        if (length(CP1s) > 0 | length(CP1e) > 0) {
694 
+        if (length(CP1s) > 0 | length(CP1e) >
695 
+            0) {
524 696 
             CC <- c(CP1s, CP1e)
525 
-            Events[[ii]]$P1 <- Events[[ii]]$P1[-CC, ]
697 
+            Events[[ii]]$P1 <- Events[[ii]]$P1[-CC,
698 
+                ]
526 699 
         }
527 700
528 
-        PS1 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P1[, 1]))
529 
-        PE1 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P1[, 2]))
701 
+        PS1 <- as.numeric(gsub(".[ab]", "",
702 
+            Events[[ii]]$P1[, 1]))
703 
+        PE1 <- as.numeric(gsub(".[ab]", "",
704 
+            Events[[ii]]$P1[, 2]))
530 705 
         Path1 <- as.matrix(cbind(PS1, PE1))
531 
-        Path1 <- Path1[order(Path1[, 1], Path1[, 2]), , drop = FALSE]
706 
+        Path1 <- Path1[order(Path1[, 1],
707 
+            Path1[, 2]), , drop = FALSE]
532 708
533 
-        CP2s <- which(Events[[ii]]$P2[, 1] == "S")
534 
-        CP2e <- which(Events[[ii]]$P2[, 2] == "E")
709 
+        CP2s <- which(Events[[ii]]$P2[, 1] ==
710 
+            "S")
711 
+        CP2e <- which(Events[[ii]]$P2[, 2] ==
712 
+            "E")
535 713
536 
-        if (length(CP2s) > 0 | length(CP2e) > 0) {
714 
+        if (length(CP2s) > 0 | length(CP2e) >
715 
+            0) {
537 716 
             CC <- c(CP2s, CP2e)
538 
-            Events[[ii]]$P2 <- Events[[ii]]$P2[-CC, ]
717 
+            Events[[ii]]$P2 <- Events[[ii]]$P2[-CC,
718 
+                ]
539 719 
         }
540 720
541 
-        PS2 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P2[, 1]))
542 
-        PE2 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P2[, 2]))
721 
+        PS2 <- as.numeric(gsub(".[ab]", "",
722 
+            Events[[ii]]$P2[, 1]))
723 
+        PE2 <- as.numeric(gsub(".[ab]", "",
724 
+            Events[[ii]]$P2[, 2]))
543 725 
         Path2 <- as.matrix(cbind(PS2, PE2))
544 
-        Path2 <- Path2[order(Path2[, 1], Path2[, 2]), , drop = FALSE]
726 
+        Path2 <- Path2[order(Path2[, 1],
727 
+            Path2[, 2]), , drop = FALSE]
545 728
546 
-        CPRs <- which(Events[[ii]]$Ref[, 1] == "S")
547 
-        CPRe <- which(Events[[ii]]$Ref[, 2] == "E")
729 
+        CPRs <- which(Events[[ii]]$Ref[,
730 
+            1] == "S")
731 
+        CPRe <- which(Events[[ii]]$Ref[,
732 
+            2] == "E")
548 733
549 
-        if (length(CPRs) > 0 | length(CPRe) > 0) {
734 
+        if (length(CPRs) > 0 | length(CPRe) >
735 
+            0) {
550 736 
             CC <- c(CPRs, CPRe)
551 
-            Events[[ii]]$Ref <- Events[[ii]]$Ref[-CC, ]
737 
+            Events[[ii]]$Ref <- Events[[ii]]$Ref[-CC,
738 
+                ]
552 739 
         }
553 740
554 
-        PSR <- as.numeric(gsub(".[ab]", "", Events[[ii]]$Ref[, 1]))
555 
-        PER <- as.numeric(gsub(".[ab]", "", Events[[ii]]$Ref[, 2]))
741 
+        PSR <- as.numeric(gsub(".[ab]", "",
742 
+            Events[[ii]]$Ref[, 1]))
743 
+        PER <- as.numeric(gsub(".[ab]", "",
744 
+            Events[[ii]]$Ref[, 2]))
556 745 
         PathR <- as.matrix(cbind(PSR, PER))
557 
-        PathR <- PathR[order(PathR[, 1], PathR[, 2]), , drop = FALSE]
746 
+        PathR <- PathR[order(PathR[, 1],
747 
+            PathR[, 2]), , drop = FALSE]
558 748
559 749
560 
-        Path1 <- paste(Path1[, 1], "-", Path1[, 2], sep = "", collapse = ",")
561 
-        Path2 <- paste(Path2[, 1], "-", Path2[, 2], sep = "", collapse = ",")
562 
-        PathR <- paste(PathR[, 1], "-", PathR[, 2], sep = "", collapse = ",")
750 
+        Path1 <- paste(Path1[, 1], "-", Path1[,
751 
+            2], sep = "", collapse = ",")
752 
+        Path2 <- paste(Path2[, 1], "-", Path2[,
753 
+            2], sep = "", collapse = ",")
754 
+        PathR <- paste(PathR[, 1], "-", PathR[,
755 
+            2], sep = "", collapse = ",")
563 756
564 
-        NEv <- data.frame(EventID, GeneName, EventNumber, EventType, GPos, Path1,
565 
-            Path2, PathR, stringsAsFactors = FALSE)
757 
+        NEv <- data.frame(EventID, GeneName,
758 
+            EventNumber, EventType, GPos,
759 
+            Path1, Path2, PathR, stringsAsFactors = FALSE)
566 760 
         Result[[ii]] <- NEv
567 
-
568 761 
     }
569 762
570 763 
     Result <- do.call(rbind, Result)
571 
-    colnames(Result) <- c("EventID", "Gene", "Event Number", "Event Type", "Genomic Position",
764 
+    colnames(Result) <- c("EventID", "Gene",
765 
+        "Event Number", "Event Type", "Genomic Position",
572 766 
         "Path 1", "Path 2", "Path Reference")
573 767
574 768 
     return(Result)
575 
-
576 
-
577 769 
 }
578 770
579 771 
 #' @rdname InternalFunctions
580 
-AnnotateEvents_RNASeq_MultiPath <- function(Events, paths) {
772 
+AnnotateEvents_RNASeq_MultiPath <- function(Events,
773 
+    paths) {
774 
+    Positions <- NULL
581 775 
     Result <- vector("list", length = length(Events))
582 776 
     for (ii in seq_along(Events)) {
583 
-
584 
-
585 777 
         GeneName <- as.vector(Events[[ii]]$GeneName)
586 778 
         GeneID <- as.vector(Events[[ii]]$Gene)
587 779 
         EventNumber <- ii
588 
-        EventID <- paste(GeneID, "_", EventNumber, sep = "")
780 
+        EventID <- paste(GeneID, "_", EventNumber,
781 
+            sep = "")
589 782 
         EventType <- Events[[ii]]$Type
590 
-        Chrom <- as.vector(Events[[ii]]$P1[1, "Chr"])
783 
+        Chrom <- as.vector(Events[[ii]]$P1[1,
784 
+            "Chr"])
591 785
592 786 
         EventNumP <- Events[[ii]]$NumP
593 787 
         command <- "Positions<-rbind(Events[[ii]]$P1,"
594 788 
         for (kk in 2:EventNumP) {
595 789 
             if (kk == EventNumP) {
596 
-                command <- paste0(command, "Events[[ii]]$P", kk, ")[,4:5]")
790 
+                command <- paste0(command,
791 
+                  "Events[[ii]]$P", kk, ")[,4:5]")
597 792 
             } else {
598 
-                command <- paste0(command, "Events[[ii]]$P", kk, ",")
793 
+                command <- paste0(command,
794 
+                  "Events[[ii]]$P", kk, ",")
599 795 
             }
600 796 
         }
601 797 
         eval(parse(text = command))
... ... 
@@ -608,27 +804,37 @@ AnnotateEvents_RNASeq_MultiPath <- function(Events, paths) {
608 804 
         # browser()
609 805 
         minGPos <- min(Start)
610 806 
         maxGPos <- max(End)
611 
-        GPos <- paste(Chrom, ":", minGPos, "-", maxGPos, sep = "")
612 
-
613 
-        # CP1s<-which(Events[[ii]]$P1[,1]=='S') CP1e<-which(Events[[ii]]$P1[,2]=='E')
614 
-        # if(length(CP1s)>0|length(CP1e)>0) { CC<-c(CP1s,CP1e)
615 
-        # Events[[ii]]$P1<-Events[[ii]]$P1[-CC,] }
807 
+        GPos <- paste(Chrom, ":", minGPos,
808 
+            "-", maxGPos, sep = "")
809 
+
810 
+        # CP1s<-which(Events[[ii]]$P1[,1]=='S')
811 
+        # CP1e<-which(Events[[ii]]$P1[,2]=='E')
812 
+        # if(length(CP1s)>0|length(CP1e)>0) {
813 
+        # CC<-c(CP1s,CP1e)
814 
+        # Events[[ii]]$P1<-Events[[ii]]$P1[-CC,]
815 
+        # }
616 816 
         # PS1<-as.numeric(gsub('.[ab]','',Events[[ii]]$P1[,1]))
617 817 
         # PE1<-as.numeric(gsub('.[ab]','',Events[[ii]]$P1[,2]))
618 818 
         # Path1<-as.matrix(cbind(PS1,PE1))
619 819 
         # Path1<-Path1[order(Path1[,1],Path1[,2]),,drop=FALSE]
620 820
621 821 
         for (kk in seq_len(EventNumP)) {
622 
-            command <- paste0("CP", kk, "s<-which(Events[[ii]]$P", kk, "[,1]=='S')")
822 
+            command <- paste0("CP", kk, "s<-which(Events[[ii]]$P",
823 
+                kk, "[,1]=='S')")
623 824 
             eval(parse(text = command))
624 
-            command <- paste0("CP", kk, "e<-which(Events[[ii]]$P", kk, "[,2]=='E')")
825 
+            command <- paste0("CP", kk, "e<-which(Events[[ii]]$P",
826 
+                kk, "[,2]=='E')")
625 827 
             eval(parse(text = command))
626 
-            a <- paste0("a<-length(CP", kk, "s)>0|length(CP", kk, "e)>0")
828 
+            a <- paste0("a<-length(CP", kk,
829 
+                "s)>0|length(CP", kk, "e)>0")
627 830 
             eval(parse(text = a))
628 831 
             if (a) {
629 
-                command <- paste0("CC<-c(CP", kk, "s,CP", kk, "e)")
832 
+                command <- paste0("CC<-c(CP",
833 
+                  kk, "s,CP", kk, "e)")
630 834 
                 eval(parse(text = command))
631 
-                command <- paste0("Events[[ii]]$P", kk, "<-Events[[ii]]$P", kk, "[-CC,]")
835 
+                command <- paste0("Events[[ii]]$P",
836 
+                  kk, "<-Events[[ii]]$P",
837 
+                  kk, "[-CC,]")
632 838 
                 eval(parse(text = command))
633 839 
             }
634 840 
             command <- paste0("PS", kk, "<-as.numeric(gsub('.[ab]','',Events[[ii]]$P",
... ... 
@@ -637,11 +843,13 @@ AnnotateEvents_RNASeq_MultiPath <- function(Events, paths) {
637 843 
             command <- paste0("PE", kk, "<-as.numeric(gsub('.[ab]','',Events[[ii]]$P",
638 844 
                 kk, "[,2]))")
639 845 
             eval(parse(text = command))
640 
-            command <- paste0("Path", kk, "<-as.matrix(cbind(PS", kk, ",PE", kk,
641 
-                "))")
846 
+            command <- paste0("Path", kk,
847 
+                "<-as.matrix(cbind(PS", kk,
848 
+                ",PE", kk, "))")
642 849 
             eval(parse(text = command))
643 
-            command <- paste0("Path", kk, "<-Path", kk, "[order(Path", kk, "[,1],Path",
644 
-                kk, "[,2]),,drop=FALSE]")
850 
+            command <- paste0("Path", kk,
851 
+                "<-Path", kk, "[order(Path",
852 
+                kk, "[,1],Path", kk, "[,2]),,drop=FALSE]")
645 853 
             eval(parse(text = command))
646 854 
         }
647 855
... ... 
@@ -650,26 +858,36 @@ AnnotateEvents_RNASeq_MultiPath <- function(Events, paths) {
650 858
651 859
652 860
653 
-        # CP2s<-which(Events[[ii]]$P2[,1]=='S') CP2e<-which(Events[[ii]]$P2[,2]=='E')
654 
-        # if(length(CP2s)>0|length(CP2e)>0) { CC<-c(CP2s,CP2e)
655 
-        # Events[[ii]]$P2<-Events[[ii]]$P2[-CC,] }
861 
+        # CP2s<-which(Events[[ii]]$P2[,1]=='S')
862 
+        # CP2e<-which(Events[[ii]]$P2[,2]=='E')
863 
+        # if(length(CP2s)>0|length(CP2e)>0) {
864 
+        # CC<-c(CP2s,CP2e)
865 
+        # Events[[ii]]$P2<-Events[[ii]]$P2[-CC,]
866 
+        # }
656 867 
         # PS2<-as.numeric(gsub('.[ab]','',Events[[ii]]$P2[,1]))
657 868 
         # PE2<-as.numeric(gsub('.[ab]','',Events[[ii]]$P2[,2]))
658 869 
         # Path2<-as.matrix(cbind(PS2,PE2))
659 870 
         # Path2<-Path2[order(Path2[,1],Path2[,2]),,drop=FALSE]
660 871
661 
-        CPRs <- which(Events[[ii]]$Ref[, 1] == "S")
662 
-        CPRe <- which(Events[[ii]]$Ref[, 2] == "E")
872 
+        CPRs <- which(Events[[ii]]$Ref[,
873 
+            1] == "S")
874 
+        CPRe <- which(Events[[ii]]$Ref[,
875 
+            2] == "E")
663 876
664 
-        if (length(CPRs) > 0 | length(CPRe) > 0) {
877 
+        if (length(CPRs) > 0 | length(CPRe) >
878 
+            0) {
665 879 
             CC <- c(CPRs, CPRe)
666 
-            Events[[ii]]$Ref <- Events[[ii]]$Ref[-CC, ]
880 
+            Events[[ii]]$Ref <- Events[[ii]]$Ref[-CC,
881 
+                ]
667 882 
         }
668 883
669 
-        PSR <- as.numeric(gsub(".[ab]", "", Events[[ii]]$Ref[, 1]))
670 
-        PER <- as.numeric(gsub(".[ab]", "", Events[[ii]]$Ref[, 2]))
884 
+        PSR <- as.numeric(gsub(".[ab]", "",
885 
+            Events[[ii]]$Ref[, 1]))
886 
+        PER <- as.numeric(gsub(".[ab]", "",
887 
+            Events[[ii]]$Ref[, 2]))
671 888 
         PathR <- as.matrix(cbind(PSR, PER))
672 
-        PathR <- PathR[order(PathR[, 1], PathR[, 2]), , drop = FALSE]
889 
+        PathR <- PathR[order(PathR[, 1],
890 
+            PathR[, 2]), , drop = FALSE]
673 891
674 892
675 893 
         # Path1<-paste(Path1[,1],'-',Path1[,2],sep='',collapse=',')
... ... 
@@ -677,29 +895,34 @@ AnnotateEvents_RNASeq_MultiPath <- function(Events, paths) {
677 895 
         NEv <- "NEv<-data.frame(EventID,GeneName,EventNumber,EventType,GPos,EventNumP,"
678 896 
         for (kk in seq_len(paths)) {
679 897 
             if (kk <= EventNumP) {
680 
-                command <- paste0("Path", kk, "<-paste(Path", kk, "[,1],'-',Path",
681 
-                  kk, "[,2],sep='',collapse=',')")
898 
+                command <- paste0("Path",
899 
+                  kk, "<-paste(Path", kk,
900 
+                  "[,1],'-',Path", kk, "[,2],sep='',collapse=',')")
682 901 
                 eval(parse(text = command))
683 902 
                 # command <-
684 
-                # paste0('ProbesP',kk,'<-paste(Events[[ii]]$Probes_P',kk,',collapse=',')')
685 
-                # eval(parse(text = command))
903 
+                # paste0('ProbesP',kk,'<-paste(Events[[ii]]$Probes_P',
904 
+                # kk,',collapse=',')') eval(parse(text =
905 
+                # command))
686 906 
             } else {
687 
-                command <- paste0("Path", kk, "<-'-'")
907 
+                command <- paste0("Path",
908 
+                  kk, "<-'-'")
688 909 
                 eval(parse(text = command))
689 
-                # command <- paste0('ProbesP',kk,'<-'-'') eval(parse(text = command))
910 
+                # command <- paste0('ProbesP',kk,'<-'-'')
911 
+                # eval(parse(text = command))
690 912 
             }
691 
-            NEv <- paste0(NEv, "Path", kk, ",")
913 
+            NEv <- paste0(NEv, "Path", kk,
914 
+                ",")
692 915 
         }
693 916
694 
-        PathR <- paste(PathR[, 1], "-", PathR[, 2], sep = "", collapse = ",")
917 
+        PathR <- paste(PathR[, 1], "-", PathR[,
918 
+            2], sep = "", collapse = ",")
695 919 
         NEv <- paste0(NEv, "PathR,stringsAsFactors = FALSE)")
696 920 
         eval(parse(text = NEv))
697 921 
         rownames(NEv) <- NULL
698 
-        # NEv<-data.frame(EventID,GeneName,EventNumber,EventType,GPos,Path1,Path2,PathR,stringsAsFactors
699 
-        # = FALSE)
922 
+        # NEv<-data.frame(EventID,GeneName,EventNumber,EventType,GPos,
923 
+        # Path1,Path2,PathR,stringsAsFactors =
924 
+        # FALSE)
700 925 
         Result[[ii]] <- NEv
701 
-
702 
-
703 926 
     }
704 927
705 928 
     Result <- do.call(rbind, Result)
... ... 
@@ -709,127 +932,168 @@ AnnotateEvents_RNASeq_MultiPath <- function(Events, paths) {
709 932 
         if (kk == (paths + 1)) {
710 933 
             command <- paste0(command, "'Path Ref')")
711 934 
         } else {
712 
-            command <- paste0(command, "'Path ", kk, "',")
935 
+            command <- paste0(command, "'Path ",
936 
+                kk, "',")
713 937 
         }
714 938 
     }
715 939 
     eval(parse(text = command))
716 940 
     return(Result)
717 
-
718 
-
719 941 
 }
720 942
721 943 
 #' @rdname InternalFunctions
722 
-AnnotateEvents_KLL <- function(Events, Gxx, GenI) {
944 
+AnnotateEvents_KLL <- function(Events, Gxx,
945 
+    GenI) {
723 946 
     {
724 947 
         # Gxx <- GeneName
725 948 
         GeneName <- Gxx
726 949 
         GeneID <- GenI
727 
-        Chrom <- gsub("chr", "", as.vector(Events[[1]]$P1[1, "Chr"]))
950 
+        Chrom <- gsub("chr", "", as.vector(Events[[1]]$P1[1,
951 
+            "Chr"]))
728 952 
         Result <- vector("list")
729 953 
         # Flat<-vector('list')
730 954 
         mm <- 0
731 955
732 956 
         for (ii in seq_along(Events)) {
733 
-            if (!any(c(identical(unique(Events[[ii]]$P1$Type), "V"), identical(unique(Events[[ii]]$P2$Type),
734 
-                "V"), identical(unique(Events[[ii]]$Ref$Type), "V")) == TRUE)) {
957 
+            if (!any(c(identical(unique(Events[[ii]]$P1$Type),
958 
+                "V"), identical(unique(Events[[ii]]$P2$Type),
959 
+                "V"), identical(unique(Events[[ii]]$Ref$Type),
960 
+                "V")) == TRUE)) {
735 961 
                 mm <- mm + 1
736 962
737 963 
                 EventNumber <- ii
738 964
739 965 
                 EventType <- Events[[ii]]$Type
740 966
741 
-                Positions <- rbind(Events[[ii]]$P1, Events[[ii]]$P2)[, 4:5]
742 
-                Start <- as.numeric(Positions[, 1])
743 
-                End <- as.numeric(Positions[, 2])
744 
-                Start <- Start[which(Start != 0)]
967 
+                Positions <- rbind(Events[[ii]]$P1,
968 
+                  Events[[ii]]$P2)[, 4:5]
969 
+                Start <- as.numeric(Positions[,
970 
+                  1])
971 
+                End <- as.numeric(Positions[,
972 
+                  2])
973 
+                Start <- Start[which(Start !=
974 
+                  0)]
745 975 
                 End <- End[which(End != 0)]
746 976
747 977 
                 # browser()
748 978 
                 minGPos <- min(Start)
749 979 
                 maxGPos <- max(End)
750 
-                GPos <- paste(Chrom, ":", minGPos, "-", maxGPos, sep = "")
980 
+                GPos <- paste(Chrom, ":",
981 
+                  minGPos, "-", maxGPos,
982 
+                  sep = "")
751 983
752 
-                CP1s <- which(Events[[ii]]$P1[, 1] == "S")
753 
-                CP1e <- which(Events[[ii]]$P1[, 2] == "E")
984 
+                CP1s <- which(Events[[ii]]$P1[,
985 
+                  1] == "S")
986 
+                CP1e <- which(Events[[ii]]$P1[,
987 
+                  2] == "E")
754 988
755 
-                if (length(CP1s) > 0 | length(CP1e) > 0) {
989 
+                if (length(CP1s) > 0 | length(CP1e) >
990 
+                  0) {
756 991 
                   CC <- c(CP1s, CP1e)
757 
-                  Events[[ii]]$P1 <- Events[[ii]]$P1[-CC, ]
992 
+                  Events[[ii]]$P1 <- Events[[ii]]$P1[-CC,
993 
+                    ]
758 994 
                 }
759 995
760 
-                PS1 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P1[, 1]))
761 
-                PE1 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P1[, 2]))
762 
-                Path1 <- as.matrix(cbind(PS1, PE1))
763 
-                Path1 <- Path1[order(Path1[, 1], Path1[, 2]), , drop = FALSE]
996 
+                PS1 <- as.numeric(gsub(".[ab]",
997 
+                  "", Events[[ii]]$P1[, 1]))
998 
+                PE1 <- as.numeric(gsub(".[ab]",
999 
+                  "", Events[[ii]]$P1[, 2]))
1000 
+                Path1 <- as.matrix(cbind(PS1,
1001 
+                  PE1))
1002 
+                Path1 <- Path1[order(Path1[,
1003 
+                  1], Path1[, 2]), , drop = FALSE]
764 1004
765 
-                CP2s <- which(Events[[ii]]$P2[, 1] == "S")
766 
-                CP2e <- which(Events[[ii]]$P2[, 2] == "E")
1005 
+                CP2s <- which(Events[[ii]]$P2[,
1006 
+                  1] == "S")
1007 
+                CP2e <- which(Events[[ii]]$P2[,
1008 
+                  2] == "E")
767 1009
768 
-                if (length(CP2s) > 0 | length(CP2e) > 0) {
1010 
+                if (length(CP2s) > 0 | length(CP2e) >
1011 
+                  0) {
769 1012 
                   CC <- c(CP2s, CP2e)
770 
-                  Events[[ii]]$P2 <- Events[[ii]]$P2[-CC, ]
1013 
+                  Events[[ii]]$P2 <- Events[[ii]]$P2[-CC,
1014 
+                    ]
771 1015 
                 }
772 1016
773 
-                PS2 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P2[, 1]))
774 
-                PE2 <- as.numeric(gsub(".[ab]", "", Events[[ii]]$P2[, 2]))
775 
-                Path2 <- as.matrix(cbind(PS2, PE2))
776 
-                Path2 <- Path2[order(Path2[, 1], Path2[, 2]), , drop = FALSE]
1017 
+                PS2 <- as.numeric(gsub(".[ab]",
1018 
+                  "", Events[[ii]]$P2[, 1]))
1019 
+                PE2 <- as.numeric(gsub(".[ab]",
1020 
+                  "", Events[[ii]]$P2[, 2]))
1021 
+                Path2 <- as.matrix(cbind(PS2,
1022 
+                  PE2))
1023 
+                Path2 <- Path2[order(Path2[,
1024 
+                  1], Path2[, 2]), , drop = FALSE]
777 1025
778 
-                CPRs <- which(Events[[ii]]$Ref[, 1] == "S")
779 
-                CPRe <- which(Events[[ii]]$Ref[, 2] == "E")
1026 
+                CPRs <- which(Events[[ii]]$Ref[,
1027 
+                  1] == "S")
1028 
+                CPRe <- which(Events[[ii]]$Ref[,
1029 
+                  2] == "E")
780