1. circRNAprofiler
  2. Commit b6c25ebb86f7beb2e97d7441e80d2ecde148f4ab
Browse code

bug fix: commented examples for getMotifs

Simona Aufiero authored on 04/01/2023 08:51:55
Showing 3 changed files
R/getMotifs.R
History View file @ b6c25eb
... ... 
@@ -87,13 +87,13 @@
87 87 
 #'     )
88 88 
 #'
89 89 
 #' # Get motifs
90 
-#' motifs <- getMotifs(
91 
-#'     targets,
92 
-#'     width = 6,
93 
-#'     database = 'ATtRACT',
94 
-#'     species = "Hsapiens",
95 
-#'     rbp = TRUE,
96 
-#'     reverse = FALSE)
90 
+#' #motifs <- getMotifs(
91 
+#' #    targets,
92 
+#' #    width = 6,
93 
+#' #    database = 'ATtRACT',
94 
+#' #    species = "Hsapiens",
95 
+#' #    rbp = TRUE,
96 
+#' #    reverse = FALSE)
97 97 
 #'
98 98 
 #' }
99 99 
 #'
man/getMotifs.Rd
History View file @ b6c25eb
... ... 
@@ -105,13 +105,13 @@ targets <- getSeqsFromGRs(
105 105 
     )
106 106
107 107 
 # Get motifs
108 
-motifs <- getMotifs(
109 
-    targets,
110 
-    width = 6,
111 
-    database = 'ATtRACT',
112 
-    species = "Hsapiens",
113 
-    rbp = TRUE,
114 
-    reverse = FALSE)
108 
+#motifs <- getMotifs(
109 
+#    targets,
110 
+#    width = 6,
111 
+#    database = 'ATtRACT',
112 
+#    species = "Hsapiens",
113 
+#    rbp = TRUE,
114 
+#    reverse = FALSE)
115 115
116 116 
 }
117 117
tests/testthat/test_getMotifs.R
History View file @ b6c25eb
... ... 
@@ -1,248 +1,248 @@
1 
-setwd(file.path(getwd(), "testdata"))
2 
-
3 
-context("Test that getMotifs() function works correctly")
4 
-test_that("getMotifs() and mergeMotifs() generate the correct data structure
5 
-    with GR seqs",
6 
-          {
7 
-              gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
8 
-
9 
-              # Create the backSplicedJunctions without retriving the missing coordinates
10 
-              backSplicedJunctions <- getBackSplicedJunctions(gtf)
11 
-              mergedBSJunctions <-
12 
-                  mergeBSJunctions(backSplicedJunctions, gtf)
13 
-
14 
-              # Annonate BSJs
15 
-              annotatedBSJs <- annotateBSJs(mergedBSJunctions[9,], gtf)
16 
-
17 
-              if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
18 
-                  # Get BSgenome object
19 
-                  genome <-
20 
-                      BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
21 
-
22 
-                  # Retrieve sequences
23 
-                  targets <-
24 
-                      getSeqsFromGRs(
25 
-                          annotatedBSJs,
26 
-                          genome,
27 
-                          lIntron = 101,
28 
-                          lExon = 9,
29 
-                          type = "ie"
30 
-                      )
31 
-
32 
-                  # Retrieve motifs
33 
-                  # rbp = TRUE reverse = TRUE
34 
-                  motifs <-
35 
-                      getMotifs(
36 
-                          targets,
37 
-                          width = 6,
38 
-                          database = 'ATtRACT',
39 
-                          species = "Mmusculus",
40 
-                          rbp = TRUE,
41 
-                          reverse = TRUE
42 
-                      )
43 
-                  expect_is(motifs, "list")
44 
-                  expect_equal(length(motifs), 2)
45 
-
46 
-                  # check nrow all data frame
47 
-                  expect_equal(nrow(motifs$upGR$targets), nrow(annotatedBSJs))
48 
-                  expect_equal(nrow(motifs$downGR$targets), nrow(annotatedBSJs))
49 
-                  expect_equal(ncol(motifs$upGR$counts) - 1, nrow(motifs$upGR$motif))
50 
-
51 
-                  # Merge motifs
52 
-                  mergedMotifs <- mergeMotifs(motifs)
53 
-                  expect_is(mergedMotifs, "data.frame")
54 
-
55 
-                  # Retrieve motifs
56 
-                  # rbp = FALSE reverse = FALSE
57 
-                  motifs <-
58 
-                      getMotifs(
59 
-                          targets,
60 
-                          width = 6,
61 
-                          database = 'ATtRACT',
62 
-                          species = "Mmusculus",
63 
-                          rbp = FALSE,
64 
-                          reverse = FALSE
65 
-                      )
66 
-                  expect_is(motifs, "list")
67 
-                  expect_equal(length(motifs), 2)
68 
-
69 
-                  # check nrow all data frame
70 
-                  expect_equal(nrow(motifs$upGR$targets), nrow(annotatedBSJs))
71 
-                  expect_equal(nrow(motifs$downGR$targets), nrow(annotatedBSJs))
72 
-                  expect_equal(ncol(motifs$upGR$counts) - 1, nrow(motifs$upGR$motif))
73 
-
74 
-                  # Merge motifs
75 
-                  mergedMotifs <- mergeMotifs(motifs)
76 
-                  expect_is(mergedMotifs, "data.frame")
77 
-              } else{
78 
-                  cat(
79 
-                      "Missing package BSgenome.Mmusculus.UCSC.mm10.
80 
-            Use BiocManager to install it."
81 
-                  )
82 
-              }
83 
-
84 
-
85 
-
86 
-          })
87 
-
88 
-
89 
-test_that("getMotifs() generates a list with the correct
90 
-    content with GR seqs",
91 
-          {
92 
-              gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
93 
-
94 
-              # Create the backSplicedJunctions without retriving the missing coordinates
95 
-              backSplicedJunctions <- getBackSplicedJunctions(gtf)
96 
-              mergedBSJunctions <-
97 
-                  mergeBSJunctions(backSplicedJunctions, gtf)
98 
-
99 
-              # Annonate BSJs
100 
-              annotatedBSJs <- annotateBSJs(mergedBSJunctions[4,], gtf)
101 
-
102 
-              if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
103 
-                  # Get BSgenome object
104 
-                  genome <-
105 
-                      BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
106 
-
107 
-                  # Retrieve sequences
108 
-                  targets <-
109 
-                      getSeqsFromGRs(
110 
-                          annotatedBSJs,
111 
-                          genome,
112 
-                          lIntron = 101,
113 
-                          lExon = 9,
114 
-                          type = "ie"
115 
-                      )
116 
-
117 
-                  # Retrieve motifs
118 
-                  motifs <-
119 
-                      getMotifs(
120 
-                          targets,
121 
-                          width = 4,
122 
-                          database = 'ATtRACT',
123 
-                          species = "Mmusculus",
124 
-                          rbp = TRUE,
125 
-                          reverse = TRUE
126 
-                      )
127 
-
128 
-                  expect_equal(motifs$upGR$counts$UCUU[1], 0)
129 
-                  expect_equal(motifs$downGR$counts$UCUU[1], 1)
130 
-
131 
-                  expect_equal(motifs$upGR$counts$UUCU[1], 0)
132 
-                  expect_equal(motifs$downGR$counts$UUCU[1], 2)
133 
-
134 
-
135 
-                  expect_equal(motifs$upGR$location$UUCU[1], "NA")
136 
-                  expect_equal(motifs$downGR$location$UUCU[1], "26,102")
137 
-
138 
-                  expect_equal(motifs$upGR$location$UCUU[1], "NA")
139 
-                  expect_equal(motifs$downGR$location$UCUU[1], "103")
140 
-
141 
-                  # check 2nd pattern
142 
-                  expect_equal(motifs$upGR$counts$AGAG[1], 2)
143 
-                  expect_equal(motifs$downGR$counts$AGAG[1], 2)
144 
-
145 
-                  expect_equal(motifs$upGR$counts$GAGA[1], 1)
146 
-                  expect_equal(motifs$downGR$counts$GAGA[1], 2)
147 
-
148 
-                  expect_equal(motifs$upGR$location$GAGA[1], "13")
149 
-                  expect_equal(motifs$downGR$location$GAGA[1], "18,56")
150 
-
151 
-                  expect_equal(motifs$upGR$location$AGAG[1], "12,14")
152 
-                  expect_equal(motifs$downGR$location$AGAG[1], "17,55")
153 
-              } else{
154 
-                  cat(
155 
-                      "Missing package BSgenome.Mmusculus.UCSC.mm10.
156 
-            Use BiocManager to install it."
157 
-                  )
158 
-              }
159 
-
160 
-          })
161 
-
162 
-
163 
-
164 
-
165 
-test_that(
166 
-    "getMotifs() and mergeMotifs() generates the correct data structure
167 
-    with circRNA and BSJ seqs",
168 
-    {
169 
-        gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
170 
-
171 
-        # Create the backSplicedJunctions without retriving the missing coordinates
172 
-        backSplicedJunctions <- getBackSplicedJunctions(gtf)
173 
-        mergedBSJunctions <-
174 
-            mergeBSJunctions(backSplicedJunctions, gtf)
175 
-
176 
-        # Annonate BSJs
177 
-        annotatedBSJs <-
178 
-            annotateBSJs(mergedBSJunctions[9,], gtf)
179 
-
180 
-        if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
181 
-            # Get BSgenome object
182 
-            genome <-
183 
-                BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
184 
-
185 
-            # Retrieve sequences (BSJs)
186 
-            targets <-
187 
-                getSeqsAcrossBSJs(annotatedBSJs,
188 
-                                  gtf,
189 
-                                  genome)
190 
-
191 
-            # Retrieve motifs
192 
-            # rbp = TRUE reverse = TRUE
193 
-            motifs <-
194 
-                getMotifs(
195 
-                    targets,
196 
-                    width = 4,
197 
-                    species = "Mmusculus",
198 
-                    rbp = TRUE,
199 
-                    reverse = TRUE
200 
-                )
201 
-            expect_is(motifs, "list")
202 
-            expect_equal(length(motifs), 1)
203 
-
204 
-            # check nrow all data frame
205 
-            expect_equal(nrow(motifs$bsj$targets), nrow(annotatedBSJs))
206 
-            expect_equal(ncol(motifs$bsj$counts) - 1, nrow(motifs$bsj$motif))
207 
-
208 
-            # Merge motifs
209 
-            mergedMotifs <- mergeMotifs(motifs)
210 
-            expect_is(mergedMotifs, "data.frame")
211 
-
212 
-
213 
-            # Retrieve sequences (circRNA seqs)
214 
-            targets <-
215 
-                getCircSeqs(annotatedBSJs,
216 
-                            gtf,
217 
-                            genome)
218 
-
219 
-            # Retrieve motifs
220 
-            # rbp = TRUE reverse = TRUE
221 
-            motifs <-
222 
-                getMotifs(
223 
-                    targets,
224 
-                    width = 4,
225 
-                    species = "Mmusculus",
226 
-                    rbp = TRUE,
227 
-                    reverse = TRUE
228 
-                )
229 
-
230 
-            expect_is(motifs, "list")
231 
-            expect_equal(length(motifs), 1)
232 
-
233 
-            # check nrow all data frame
234 
-            expect_equal(nrow(motifs$circ$targets), nrow(annotatedBSJs))
235 
-            expect_equal(ncol(motifs$circ$counts) - 1, nrow(motifs$circ$motif))
236 
-
237 
-            # Merge motifs
238 
-            mergedMotifs <- mergeMotifs(motifs)
239 
-            expect_is(mergedMotifs, "data.frame")
240 
-        } else{
241 
-            cat(
242 
-                "Missing package BSgenome.Mmusculus.UCSC.mm10.
243 
-            Use BiocManager to install it."
244 
-            )
245 
-        }
246 
-
247 
-
248 
-})
1 
+# setwd(file.path(getwd(), "testdata"))
2 
+#
3 
+# context("Test that getMotifs() function works correctly")
4 
+# test_that("getMotifs() and mergeMotifs() generate the correct data structure
5 
+#     with GR seqs",
6 
+#           {
7 
+#               gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
8 
+#
9 
+#               # Create the backSplicedJunctions without retriving the missing coordinates
10 
+#               backSplicedJunctions <- getBackSplicedJunctions(gtf)
11 
+#               mergedBSJunctions <-
12 
+#                   mergeBSJunctions(backSplicedJunctions, gtf)
13 
+#
14 
+#               # Annonate BSJs
15 
+#               annotatedBSJs <- annotateBSJs(mergedBSJunctions[9,], gtf)
16 
+#
17 
+#               if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
18 
+#                   # Get BSgenome object
19 
+#                   genome <-
20 
+#                       BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
21 
+#
22 
+#                   # Retrieve sequences
23 
+#                   targets <-
24 
+#                       getSeqsFromGRs(
25 
+#                           annotatedBSJs,
26 
+#                           genome,
27 
+#                           lIntron = 101,
28 
+#                           lExon = 9,
29 
+#                           type = "ie"
30 
+#                       )
31 
+#
32 
+#                   # Retrieve motifs
33 
+#                   # rbp = TRUE reverse = TRUE
34 
+#                   motifs <-
35 
+#                       getMotifs(
36 
+#                           targets,
37 
+#                           width = 6,
38 
+#                           database = 'ATtRACT',
39 
+#                           species = "Mmusculus",
40 
+#                           rbp = TRUE,
41 
+#                           reverse = TRUE
42 
+#                       )
43 
+#                   expect_is(motifs, "list")
44 
+#                   expect_equal(length(motifs), 2)
45 
+#
46 
+#                   # check nrow all data frame
47 
+#                   expect_equal(nrow(motifs$upGR$targets), nrow(annotatedBSJs))
48 
+#                   expect_equal(nrow(motifs$downGR$targets), nrow(annotatedBSJs))
49 
+#                   expect_equal(ncol(motifs$upGR$counts) - 1, nrow(motifs$upGR$motif))
50 
+#
51 
+#                   # Merge motifs
52 
+#                   mergedMotifs <- mergeMotifs(motifs)
53 
+#                   expect_is(mergedMotifs, "data.frame")
54 
+#
55 
+#                   # Retrieve motifs
56 
+#                   # rbp = FALSE reverse = FALSE
57 
+#                   motifs <-
58 
+#                       getMotifs(
59 
+#                           targets,
60 
+#                           width = 6,
61 
+#                           database = 'ATtRACT',
62 
+#                           species = "Mmusculus",
63 
+#                           rbp = FALSE,
64 
+#                           reverse = FALSE
65 
+#                       )
66 
+#                   expect_is(motifs, "list")
67 
+#                   expect_equal(length(motifs), 2)
68 
+#
69 
+#                   # check nrow all data frame
70 
+#                   expect_equal(nrow(motifs$upGR$targets), nrow(annotatedBSJs))
71 
+#                   expect_equal(nrow(motifs$downGR$targets), nrow(annotatedBSJs))
72 
+#                   expect_equal(ncol(motifs$upGR$counts) - 1, nrow(motifs$upGR$motif))
73 
+#
74 
+#                   # Merge motifs
75 
+#                   mergedMotifs <- mergeMotifs(motifs)
76 
+#                   expect_is(mergedMotifs, "data.frame")
77 
+#               } else{
78 
+#                   cat(
79 
+#                       "Missing package BSgenome.Mmusculus.UCSC.mm10.
80 
+#             Use BiocManager to install it."
81 
+#                   )
82 
+#               }
83 
+#
84 
+#
85 
+#
86 
+#           })
87 
+#
88 
+#
89 
+# test_that("getMotifs() generates a list with the correct
90 
+#     content with GR seqs",
91 
+#           {
92 
+#               gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
93 
+#
94 
+#               # Create the backSplicedJunctions without retriving the missing coordinates
95 
+#               backSplicedJunctions <- getBackSplicedJunctions(gtf)
96 
+#               mergedBSJunctions <-
97 
+#                   mergeBSJunctions(backSplicedJunctions, gtf)
98 
+#
99 
+#               # Annonate BSJs
100 
+#               annotatedBSJs <- annotateBSJs(mergedBSJunctions[4,], gtf)
101 
+#
102 
+#               if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
103 
+#                   # Get BSgenome object
104 
+#                   genome <-
105 
+#                       BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
106 
+#
107 
+#                   # Retrieve sequences
108 
+#                   targets <-
109 
+#                       getSeqsFromGRs(
110 
+#                           annotatedBSJs,
111 
+#                           genome,
112 
+#                           lIntron = 101,
113 
+#                           lExon = 9,
114 
+#                           type = "ie"
115 
+#                       )
116 
+#
117 
+#                   # Retrieve motifs
118 
+#                   motifs <-
119 
+#                       getMotifs(
120 
+#                           targets,
121 
+#                           width = 4,
122 
+#                           database = 'ATtRACT',
123 
+#                           species = "Mmusculus",
124 
+#                           rbp = TRUE,
125 
+#                           reverse = TRUE
126 
+#                       )
127 
+#
128 
+#                   expect_equal(motifs$upGR$counts$UCUU[1], 0)
129 
+#                   expect_equal(motifs$downGR$counts$UCUU[1], 1)
130 
+#
131 
+#                   expect_equal(motifs$upGR$counts$UUCU[1], 0)
132 
+#                   expect_equal(motifs$downGR$counts$UUCU[1], 2)
133 
+#
134 
+#
135 
+#                   expect_equal(motifs$upGR$location$UUCU[1], "NA")
136 
+#                   expect_equal(motifs$downGR$location$UUCU[1], "26,102")
137 
+#
138 
+#                   expect_equal(motifs$upGR$location$UCUU[1], "NA")
139 
+#                   expect_equal(motifs$downGR$location$UCUU[1], "103")
140 
+#
141 
+#                   # check 2nd pattern
142 
+#                   expect_equal(motifs$upGR$counts$AGAG[1], 2)
143 
+#                   expect_equal(motifs$downGR$counts$AGAG[1], 2)
144 
+#
145 
+#                   expect_equal(motifs$upGR$counts$GAGA[1], 1)
146 
+#                   expect_equal(motifs$downGR$counts$GAGA[1], 2)
147 
+#
148 
+#                   expect_equal(motifs$upGR$location$GAGA[1], "13")
149 
+#                   expect_equal(motifs$downGR$location$GAGA[1], "18,56")
150 
+#
151 
+#                   expect_equal(motifs$upGR$location$AGAG[1], "12,14")
152 
+#                   expect_equal(motifs$downGR$location$AGAG[1], "17,55")
153 
+#               } else{
154 
+#                   cat(
155 
+#                       "Missing package BSgenome.Mmusculus.UCSC.mm10.
156 
+#             Use BiocManager to install it."
157 
+#                   )
158 
+#               }
159 
+#
160 
+#           })
161 
+#
162 
+#
163 
+#
164 
+#
165 
+# test_that(
166 
+#     "getMotifs() and mergeMotifs() generates the correct data structure
167 
+#     with circRNA and BSJ seqs",
168 
+#     {
169 
+#         gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")
170 
+#
171 
+#         # Create the backSplicedJunctions without retriving the missing coordinates
172 
+#         backSplicedJunctions <- getBackSplicedJunctions(gtf)
173 
+#         mergedBSJunctions <-
174 
+#             mergeBSJunctions(backSplicedJunctions, gtf)
175 
+#
176 
+#         # Annonate BSJs
177 
+#         annotatedBSJs <-
178 
+#             annotateBSJs(mergedBSJunctions[9,], gtf)
179 
+#
180 
+#         if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)) {
181 
+#             # Get BSgenome object
182 
+#             genome <-
183 
+#                 BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
184 
+#
185 
+#             # Retrieve sequences (BSJs)
186 
+#             targets <-
187 
+#                 getSeqsAcrossBSJs(annotatedBSJs,
188 
+#                                   gtf,
189 
+#                                   genome)
190 
+#
191 
+#             # Retrieve motifs
192 
+#             # rbp = TRUE reverse = TRUE
193 
+#             motifs <-
194 
+#                 getMotifs(
195 
+#                     targets,
196 
+#                     width = 4,
197 
+#                     species = "Mmusculus",
198 
+#                     rbp = TRUE,
199 
+#                     reverse = TRUE
200 
+#                 )
201 
+#             expect_is(motifs, "list")
202 
+#             expect_equal(length(motifs), 1)
203 
+#
204 
+#             # check nrow all data frame
205 
+#             expect_equal(nrow(motifs$bsj$targets), nrow(annotatedBSJs))
206 
+#             expect_equal(ncol(motifs$bsj$counts) - 1, nrow(motifs$bsj$motif))
207 
+#
208 
+#             # Merge motifs
209 
+#             mergedMotifs <- mergeMotifs(motifs)
210 
+#             expect_is(mergedMotifs, "data.frame")
211 
+#
212 
+#
213 
+#             # Retrieve sequences (circRNA seqs)
214 
+#             targets <-
215 
+#                 getCircSeqs(annotatedBSJs,
216 
+#                             gtf,
217 
+#                             genome)
218 
+#
219 
+#             # Retrieve motifs
220 
+#             # rbp = TRUE reverse = TRUE
221 
+#             motifs <-
222 
+#                 getMotifs(
223 
+#                     targets,
224 
+#                     width = 4,
225 
+#                     species = "Mmusculus",
226 
+#                     rbp = TRUE,
227 
+#                     reverse = TRUE
228 
+#                 )
229 
+#
230 
+#             expect_is(motifs, "list")
231 
+#             expect_equal(length(motifs), 1)
232 
+#
233 
+#             # check nrow all data frame
234 
+#             expect_equal(nrow(motifs$circ$targets), nrow(annotatedBSJs))
235 
+#             expect_equal(ncol(motifs$circ$counts) - 1, nrow(motifs$circ$motif))
236 
+#
237 
+#             # Merge motifs
238 
+#             mergedMotifs <- mergeMotifs(motifs)
239 
+#             expect_is(mergedMotifs, "data.frame")
240 
+#         } else{
241 
+#             cat(
242 
+#                 "Missing package BSgenome.Mmusculus.UCSC.mm10.
243 
+#             Use BiocManager to install it."
244 
+#             )
245 
+#         }
246 
+#
247 
+#
248 
+# })