Mercurial > repos > eschen42 > mqppep_anova

comparison mqppep_anova_script.Rmd @ 29:42b207aaa527 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 83864e12abbf63728a389b7fe677f3b88844e03f
author eschen42
date Thu, 27 Oct 2022 22:11:38 +0000
parents 5b8e15b2a67c
children c33c30398908
comparison
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28:896eb8ae1c8c 29:42b207aaa527
104 printTraceMsgs: FALSE 104 printTraceMsgs: FALSE
105 # when debugging files are needed, set debugFileBasePath to the path 105 # when debugging files are needed, set debugFileBasePath to the path
106 # to the directory where they should be writtn 106 # to the directory where they should be writtn
107 debugFileBasePath: !r if (TRUE) NULL else "test-data" 107 debugFileBasePath: !r if (TRUE) NULL else "test-data"
108 --- 108 ---
109 <!-- 109
110 alphaFile: "test-data/alpha_levels.tabular"
111 inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
112 preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
113 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
114 regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$"
115 regexSampleGrouping: "\\w+"
116 groupFilterPatterns: ".+"
117 groupFilter: !r c("none", "exclude", "include")[3]
118 imputationMethod: !r c("group-median", "median", "mean", "random")[1]
119 kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[1]
120 ut_alphaFile: "test-data/alpha_levels.tabular"
121 ut_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
122 ut_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
123 ut_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
124 ut_regexSampleNames: "\\.\\d+[A-Z]$"
125 ut_regexSampleGrouping: "\\d+"
126 ut_groupFilterPatterns: ".+,.*"
127 ut_groupFilter: !r c("none", "exclude", "include")[1]
128 ut_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
129 ut_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1]
130 tst_alphaFile: "test-data/alpha_levels.tabular"
131 tst_inputFile: "test-data/test_input_for_anova.tabular"
132 tst_preprocDb: "test-data/test_input_for_anova.sqlite"
133 tst_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
134 tst_regexSampleNames: "\\.\\d+[A-Z]$"
135 tst_regexSampleGrouping: "\\d+"
136 tst_groupFilterPatterns: ".+"
137 tst_groupFilter: !r c("none", "exclude", "include")[1]
138 tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
139 tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5]
140
141 tst_alphaFile: "test-data/alpha_levels.tabular"
142 tst_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
143 tst_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
144 tst_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
145 tst_regexSampleNames: "\\.\\d+[A-Z]$"
146 tst_regexSampleGrouping: "\\d+"
147 tst_groupFilterPatterns: ".+,.*"
148 tst_groupFilter: !r c("none", "exclude", "include")[1]
149 tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
150 tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5]
151 px_alphaFile: "test-data/alpha_levels.tabular"
152 px_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
153 px_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
154 px_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
155 px_regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$"
156 px_regexSampleGrouping: "\\w+"
157 px_groupFilterPatterns: ".+"
158 px_groupFilter: !r c("none", "exclude", "include")[3]
159 px_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
160 px_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5]
161 pdx_alphaFile: "test-data/alpha_levels.tabular"
162 pdx_inputFile: "test-data/PDX012970_pST.preproc_tab.tabular"
163 pdx_preprocDb: "test-data/PDX012970_pST.preproc.sqlite"
164 pdx_kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2]
165 pdx_regexSampleNames: "\\.\\w+\\.\\w+\\.\\d+[A-Z]$"
166 pdx_regexSampleGrouping: "\\.\\w+\\K\\.\\w+"
167 pdx_groupFilterPatterns: "AdCa,AVPC"
168 pdx_groupFilter: !r c("none", "exclude", "include")[3]
169 pdx_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
170 pdx_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1]
171 tst_alphaFile: "test-data/alpha_levels.tabular"
172 tst_inputFile: "test-data/test_input_for_anova.tabular"
173 tst_preprocDb: "test-data/test_input_for_anova.sqlite"
174 tst_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
175 tst_regexSampleNames: "\\.\\d+[A-Z]$"
176 tst_regexSampleGrouping: "\\d+"
177 tst_groupFilterPatterns: ".+"
178 tst_groupFilter: !r c("none", "exclude", "include")[1]
179 tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5]
180 tst_imputationMethod: !r c("group-median", "median", "mean", "random")[1]
181 ut_alphaFile: "test-data/alpha_levels.tabular"
182 ut_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
183 ut_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
184 ut_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
185 ut_regexSampleNames: "\\.\\d+[A-Z]$"
186 ut_regexSampleGrouping: "\\d+"
187 ut_groupFilterPatterns: ".+,.*"
188 ut_groupFilter: !r c("none", "exclude", "include")[1]
189 ut_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
190 alphaFile: "test-data/alpha_levels.tabular"
191 inputFile: "test-data/test_input_for_anova.tabular"
192 preprocDb: "test-data/test_input_for_anova.sqlite"
193 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
194 regexSampleNames: "\\.\\d+[A-Z]$"
195 regexSampleGrouping: "\\d+"
196 groupFilterPatterns: ".+,.*"
197 groupFilter: !r c("none", "exclude", "include")[1]
198 imputationMethod: !r c("group-median", "median", "mean", "random")[4]
199 nd_alphaFile: "test-data/alpha_levels.tabular"
200 nd_inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
201 nd_preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
202 nd_kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
203 nd_regexSampleNames: "\\.\\d+[A-Z]$"
204 nd_regexSampleGrouping: "\\d+"
205 nd_groupFilterPatterns: ".+,.*"
206 nd_groupFilter: !r c("none", "exclude", "include")[1]
207 nd_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
208 pxd_alphaFile: "test-data/alpha_levels.tabular"
209 pxd_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
210 pxd_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
211 pxd_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
212 pxd_regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$"
213 pxd_regexSampleGrouping: "\\w+"
214 pxd_groupFilterPatterns: ".+"
215 pxd_groupFilter: !r c("none", "exclude", "include")[3]
216 pxd_imputationMethod: !r c("group-median", "median", "mean", "random")[4]
217
218 alphaFile: "test-data/alpha_levels.tabular"
219 inputFile: "test-data/test_input_for_anova.tabular"
220 preprocDb: "test-data/test_input_for_anova.sqlite"
221 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
222 regexSampleNames: "\\.\\d+[A-Z]$"
223 regexSampleGrouping: "\\d+"
224 groupFilterPatterns: ".+,.*"
225 groupFilter: !r c("none", "exclude", "include")[1]
226
227 alphaFile: "test-data/alpha_levels.tabular"
228 inputFile: "test-data/PDX012970_pST.preproc_tab.tabular"
229 preprocDb: "test-data/PDX012970_pST.preproc.sqlite"
230 kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2]
231 regexSampleNames: "\\.\\w+\\.\\w+\\.\\d+[A-Z]$"
232 regexSampleGrouping: "\\.\\w+\\K\\.\\w+"
233 groupFilterPatterns: "AdCa,AVPC"
234 groupFilter: !r c("none", "exclude", "include")[3]
235
236 alphaFile: "test-data/alpha_levels.tabular"
237 inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"
238 preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"
239 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]
240 regexSampleNames: "\\.\\w+\\.\\d+[A-Z]$"
241 regexSampleGrouping: "\\w+"
242 groupFilterPatterns: ".+,.*"
243 groupFilter: !r c("none", "exclude", "include")[3]
244
245 kseaCutoffStatistic: !r c("p.value", "FDR")[2]
246 kseaCutoffThreshold: !r c(0.05, 0.1)[1]
247
248 alphaFile: "test-data/alpha_levels.tabular"
249 inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"
250 preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"
251 kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]
252 regexSampleNames: "\\.\\d+[A-Z]$"
253 regexSampleGrouping: "\\d+"
254
255 alphaFile: "test-data/alpha_levels.tabular"
256 inputFile: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.tabular"
257 preprocDb: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.sqlite"
258 kseaAppPrepDb: !r c(":memory:", "test-data/pY_Sites_NancyDu.ksea.sqlite")[2]
259 regexSampleNames: "\\.\\d+[A-Z]$"
260 regexSampleGrouping: "\\d+"
261 groupFilterPatterns: ".+,.*"
262 groupFilter: !r c("none", "exclude", "include")[3]
263
264 alphaFile: "test-data/alpha_levels.tabular"
265 inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular"
266 preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"
267 kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]
268 regexSampleNames: "\\.\\d+[A-Z]$"
269 regexSampleGrouping: "\\d+"
270 groupFilterPatterns: ".+,.*"
271 groupFilter: !r c("none", "exclude", "include")[1]
272
273 -->
274 ```{r setup, include = FALSE, results = 'asis'} 110 ```{r setup, include = FALSE, results = 'asis'}
275 111
276 # simple debug messaging 112 # simple debug messaging
277 print_nb_messages <- params$printNBMsgs 113 print_nb_messages <- params$printNBMsgs
278 114