Mercurial > repos > ethevenot > checkformat
comparison checkformat_script.R @ 4:9590fac86f63 draft
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 46e92656192f2714265cc525b283c7cbb87b9093
author | ethevenot |
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date | Wed, 28 Feb 2018 05:47:44 -0500 |
parents | 80a38d36f946 |
children |
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3:80a38d36f946 | 4:9590fac86f63 |
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80 } | 80 } |
81 | 81 |
82 if(nrow(datMN) != nrow(samDF)) { | 82 if(nrow(datMN) != nrow(samDF)) { |
83 if(nrow(datMN) > nrow(samDF)) { | 83 if(nrow(datMN) > nrow(samDF)) { |
84 print(setdiff(rownames(datMN), rownames(samDF))) | 84 print(setdiff(rownames(datMN), rownames(samDF))) |
85 stop("The sample names above from dataMatrix were not found in sampleMetadata") | 85 stop("The sample names above from dataMatrix were not found in sampleMetadata", |
86 call. = FALSE) | |
86 } else { | 87 } else { |
87 print(setdiff(rownames(samDF), rownames(datMN))) | 88 print(setdiff(rownames(samDF), rownames(datMN))) |
88 stop("The sample names above from sampleMetadata were not found in dataMatrix") | 89 stop("The sample names above from sampleMetadata were not found in dataMatrix", |
90 call. = FALSE) | |
89 } | 91 } |
90 } | 92 } |
91 | 93 |
92 if(ncol(datMN) != nrow(varDF)) { | 94 if(ncol(datMN) != nrow(varDF)) { |
93 if(ncol(datMN) > nrow(varDF)) { | 95 if(ncol(datMN) > nrow(varDF)) { |
94 print(setdiff(colnames(datMN), rownames(varDF))) | 96 print(setdiff(colnames(datMN), rownames(varDF))) |
95 stop("The variable names above from dataMatrix were not found in variableMetadata") | 97 stop("The variable names above from dataMatrix were not found in variableMetadata", |
98 call. = FALSE) | |
96 } else { | 99 } else { |
97 print(setdiff(rownames(varDF), colnames(datMN))) | 100 print(setdiff(rownames(varDF), colnames(datMN))) |
98 stop("The variable names above from variableMetadata were not found in dataMatrix") | 101 stop("The variable names above from variableMetadata were not found in dataMatrix", |
102 call. = FALSE) | |
99 } | 103 } |
100 } | 104 } |
101 | 105 |
102 | 106 |
103 ## making sample and variable names (optional) | 107 ## making sample and variable names (optional) |
179 | 183 |
180 return(resLs) | 184 return(resLs) |
181 | 185 |
182 } ## end of checkAndReadF | 186 } ## end of checkAndReadF |
183 | 187 |
184 | |
185 | |
186 | |
187 ## if(!identical(rownames(datMN), rownames(samDF))) { | |
188 ## ## checking sample names | |
189 | |
190 ## chkL <- FALSE | |
191 | |
192 ## datSamDifVc <- setdiff(rownames(datMN), rownames(samDF)) | |
193 | |
194 ## if(length(datSamDifVc)) { | |
195 ## cat("\nThe following samples were found in the dataMatrix column names but not in the sampleMetadata row names:\n", sep="") | |
196 ## print(cbind.data.frame(col = as.numeric(sapply(datSamDifVc, function(samC) which(rownames(datMN) == samC))), | |
197 ## name = datSamDifVc)) | |
198 ## } | |
199 | |
200 ## samDatDifVc <- setdiff(rownames(samDF), rownames(datMN)) | |
201 | |
202 ## if(length(samDatDifVc)) { | |
203 ## cat("\n\nThe following samples were found in the sampleMetadata row names but not in the dataMatrix column names:\n", sep="") | |
204 ## print(cbind.data.frame(row = as.numeric(sapply(samDatDifVc, function(samC) which(rownames(samDF) == samC))), | |
205 ## name = samDatDifVc)) | |
206 ## } | |
207 | |
208 ## if(nrow(datMN) != nrow(samDF)) { | |
209 ## cat("\n\nThe dataMatrix has ", nrow(datMN), " columns (ie samples) whereas the sampleMetadata has ", nrow(samDF), " rows\n", sep="") | |
210 ## } else if(identical(gsub("^X", "", rownames(datMN)), rownames(samDF))) { | |
211 ## cat("\n\nThe dataMatrix column names start with an 'X' but not the sampleMetadata row names\n", sep="") | |
212 ## } else if(identical(gsub("^X", "", rownames(samDF)), rownames(datMN))) { | |
213 ## cat("\n\nThe sampleMetadata row names start with an 'X' but not the dataMatrix column names\n", sep="") | |
214 ## } else if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) { | |
215 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not in the same order:\n", sep="") | |
216 ## print(cbind.data.frame(indice = 1:nrow(datMN), | |
217 ## dataMatrix_columnnames=rownames(datMN), | |
218 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE]) | |
219 ## } else { | |
220 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not identical:\n", sep="") | |
221 ## print(cbind.data.frame(indice = 1:nrow(datMN), | |
222 ## dataMatrix_columnnames=rownames(datMN), | |
223 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE]) | |
224 ## } | |
225 | |
226 ## } | |
227 ## datRowVc <- rownames(datMN) | |
228 ## datRowMakVc <- make.names(datRowVc, unique = TRUE) | |
229 ## if(datRowMakVc != datRowVc) { | |
230 ## rownames(datMN) <- datRowMakVc | |
231 ## cat("\n\nMessage: The sample names of the dataMatrix have been converted to the standard R format\n") | |
232 ## } | |
233 | |
234 ## datColVc <- colnames(datMN) | |
235 ## datColMakVc <- make.names(datColVc, unique = TRUE) | |
236 ## if(datColMakVc != datColVc) { | |
237 ## colnames(datMN) <- datColMakVc | |
238 ## cat("\n\nMessage: The variable names of the dataMatrix have been converted to the standard R format\n") | |
239 ## } | |
240 | |
241 ## samRowVc <- rownames(datMN) | |
242 ## samRowMakVc <- make.names(samRowVc, unique = TRUE) | |
243 ## if(samRowMakVc != samRowVc) { | |
244 ## rownames(datMN) <- samRowMakVc | |
245 ## cat("\n\nMessage: The sample names of the sampleMetadata have been converted to the standard R format\n") | |
246 ## } | |
247 | |
248 ## datRowVc <- rownames(datMN) | |
249 ## datRowMakVc <- make.names(datRowVc, unique = TRUE) | |
250 ## if(datRowMakVc != datRowVc) { | |
251 ## rownames(datMN) <- datRowMakVc | |
252 ## cat("\n\nMessage: The sample names of the dataMatrix have been converted to the standard R format\n") | |
253 ## } | |
254 | |
255 ## } | |
256 | |
257 ## checking names (optional) | |
258 | |
259 | |
260 | |
261 | |
262 ## datRowMakVc <- make.names(datRowVc, unique = TRUE) | |
263 ## if(datRowMakVc != datRowVc) { | |
264 ## if(makNamL) { | |
265 ## rownames(datMN) <- datRowMakVc | |
266 ## cat("\n\nMessage: The sample names of the dataMatrix have been converted to the standard R format; select the make names argument to convert them\n") | |
267 ## } else { | |
268 ## cat("\n\nWarning: Some of the sample names of the dataMatrix are not in the standard R format; select the make names argument to convert them\n") | |
269 ## } | |
270 | |
271 ## if(makNamL) { | |
272 | |
273 ## rownames(datMN) <- make.names(rownames(datMN), unique = TRUE) | |
274 ## colnames(datMN) <- make.names(colnames(datMN), unique = TRUE) | |
275 ## rownames(samDF) <- make.names(rownames(samDF), unique = TRUE) | |
276 ## rownames(varDF) <- make.names(rownames(varDF), unique = TRUE) | |
277 | |
278 ## } | |
279 ## checking sample names | |
280 | |
281 ## if(nrow(datMN) == nrow(samDF)) { | |
282 | |
283 | |
284 | |
285 ## } | |
286 | |
287 ## chkL <- FALSE | |
288 | |
289 ## datSamDifVc <- setdiff(rownames(datMN), rownames(samDF)) | |
290 | |
291 ## if(length(datSamDifVc)) { | |
292 ## cat("\nThe following samples were found in the dataMatrix column names but not in the sampleMetadata row names:\n", sep="") | |
293 ## print(cbind.data.frame(col = as.numeric(sapply(datSamDifVc, function(samC) which(rownames(datMN) == samC))), | |
294 ## name = datSamDifVc)) | |
295 ## } | |
296 | |
297 ## samDatDifVc <- setdiff(rownames(samDF), rownames(datMN)) | |
298 | |
299 ## if(length(samDatDifVc)) { | |
300 ## cat("\n\nThe following samples were found in the sampleMetadata row names but not in the dataMatrix column names:\n", sep="") | |
301 ## print(cbind.data.frame(row = as.numeric(sapply(samDatDifVc, function(samC) which(rownames(samDF) == samC))), | |
302 ## name = samDatDifVc)) | |
303 ## } | |
304 | |
305 ## if(nrow(datMN) != nrow(samDF)) { | |
306 ## cat("\n\nThe dataMatrix has ", nrow(datMN), " columns (ie samples) whereas the sampleMetadata has ", nrow(samDF), " rows\n", sep="") | |
307 ## } else if(identical(gsub("^X", "", rownames(datMN)), rownames(samDF))) { | |
308 ## cat("\n\nThe dataMatrix column names start with an 'X' but not the sampleMetadata row names\n", sep="") | |
309 ## } else if(identical(gsub("^X", "", rownames(samDF)), rownames(datMN))) { | |
310 ## cat("\n\nThe sampleMetadata row names start with an 'X' but not the dataMatrix column names\n", sep="") | |
311 ## } else if(identical(sort(rownames(datMN)), sort(rownames(samDF)))) { | |
312 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not in the same order:\n", sep="") | |
313 ## print(cbind.data.frame(indice = 1:nrow(datMN), | |
314 ## dataMatrix_columnnames=rownames(datMN), | |
315 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE]) | |
316 ## } else { | |
317 ## cat("\n\nThe dataMatrix column names and the sampleMetadata row names are not identical:\n", sep="") | |
318 ## print(cbind.data.frame(indice = 1:nrow(datMN), | |
319 ## dataMatrix_columnnames=rownames(datMN), | |
320 ## sampleMetadata_rownames=rownames(samDF))[rownames(datMN) != rownames(samDF), , drop = FALSE]) | |
321 ## } | |
322 | |
323 ## } | |
324 | |
325 | |
326 ## if(!identical(colnames(datMN), rownames(varDF))) { | |
327 ## ## checking variable names | |
328 | |
329 ## chkL <- FALSE | |
330 | |
331 ## datVarDifVc <- setdiff(colnames(datMN), rownames(varDF)) | |
332 | |
333 ## if(length(datVarDifVc)) { | |
334 ## cat("\nThe following variables were found in the dataMatrix row names but not in the variableMetadata row names:\n", sep="") | |
335 ## print(cbind.data.frame(row = as.numeric(sapply(datVarDifVc, function(varC) which(colnames(datMN) == varC))), | |
336 ## name = datVarDifVc)) | |
337 | |
338 ## } | |
339 | |
340 ## varDatDifVc <- setdiff(rownames(varDF), colnames(datMN)) | |
341 | |
342 ## if(length(varDatDifVc)) { | |
343 ## cat("\n\nThe following variables were found in the variableMetadata row names but not in the dataMatrix row names:\n", sep="") | |
344 ## print(cbind.data.frame(row = as.numeric(sapply(varDatDifVc, function(varC) which(rownames(varDF) == varC))), | |
345 ## name = varDatDifVc)) | |
346 ## } | |
347 | |
348 ## if(ncol(datMN) != nrow(varDF)) { | |
349 ## cat("\n\nThe dataMatrix has ", nrow(datMN), " rows (ie variables) whereas the variableMetadata has ", nrow(varDF), " rows\n", sep="") | |
350 ## } else if(identical(sort(colnames(datMN)), sort(rownames(varDF)))) { | |
351 ## cat("\n\nThe dataMatrix row names and the variableMetadata row names are not in the same order:\n", sep="") | |
352 ## print(cbind.data.frame(row = 1:ncol(datMN), | |
353 ## dataMatrix_rownames=colnames(datMN), | |
354 ## variableMetadata_rownames=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE]) | |
355 ## } else { | |
356 ## cat("\n\nThe dataMatrix row names and the variableMetadata row names are not identical:\n", sep="") | |
357 ## print(cbind.data.frame(row = 1:ncol(datMN), | |
358 ## dataMatrix_rownames=colnames(datMN), | |
359 ## variableMetadata_rownames=rownames(varDF))[colnames(datMN) != rownames(varDF), , drop = FALSE]) | |
360 ## } | |
361 ## } | |
362 ## checkF <- function(datInpMN, | |
363 ## samInpDF, | |
364 ## varInpDF) { | |
365 | |
366 ## mode(datInpMN) == "numeric" && | |
367 ## identical(rownames(datInpMN), rownames(samInpDF)) && | |
368 ## identical(colnames(datInpMN), rownames(varInpDF)) | |
369 | |
370 | |
371 ## } |