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106 lines
5.2 KiB
XML
106 lines
5.2 KiB
XML
<tool id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" name="Compute P-values and Max Variances for Feature Occurrences" version="1.0.0">
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<description>in one dataset using Discrete Wavelet Transfoms</description>
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<command interpreter="perl">
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execute_dwt_var_perClass.pl $inputFile $outputFile1 $outputFile2 $outputFile3
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</command>
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<inputs>
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<param format="tabular" name="inputFile" type="data" label="Select the input file"/>
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</inputs>
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<outputs>
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<data format="tabular" name="outputFile1"/>
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<data format="tabular" name="outputFile2"/>
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<data format="pdf" name="outputFile3"/>
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</outputs>
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<help>
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.. class:: infomark
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**What it does**
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This program generates plots and computes table matrix of maximum variances, p-values, and test orientations at multiple scales for the occurrences of a class of features in one dataset of DNA sequences using multiscale wavelet analysis technique.
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The program assumes that the user has one set of DNA sequences, S, which consists of one or more sequences of equal length. Each sequence in S is divided into the same number of multiple intervals n such that n = 2^k, where k is a positive integer and k >= 1. Thus, n could be any value of the set {2, 4, 8, 16, 32, 64, 128, ...}. k represents the number of scales.
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The program has one input file obtained as follows:
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For a given set of features, say motifs, the user counts the number of occurrences of each feature in each interval of each sequence in S, and builds a tabular file representing the count results in each interval of S. This is the input file of the program.
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The program gives three output files:
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- The first output file is a TABULAR format file giving the scales at which each features has a maximum variances.
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- The second output file is a TABULAR format file representing the variances, p-values, and test orientation for the occurrences of features at each scale based on a random permutation test and using multiscale wavelet analysis technique.
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- The third output file is a PDF file plotting the wavelet variances of each feature at each scale.
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-----
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.. class:: warningmark
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**Note**
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- If the number of features is greater than 12, the program will divide each output file into subfiles, such that each subfile represents the results of a group of 12 features except the last subfile that will represents the results of the rest. For example, if the number of features is 17, the p-values file will consists of two subfiles, the first for the features 1-12 and the second for the features 13-17. As for the PDF file, it will consists of two pages in this case.
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- In order to obtain empirical p-values, a random perumtation test is implemented by the program, which results in the fact that the program gives slightly different results each time it is run on the same input file.
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-----
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**Example**
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Counting the occurrences of 8 features (motifs) in 16 intervals (one line per interval) of set of DNA sequences in S gives the following tabular file::
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deletionHoptspot insertionHoptspot dnaPolPauseFrameshift indelHotspot topoisomeraseCleavageSite translinTarget vDjRecombinationSignal x-likeSite
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226 403 416 221 1165 832 749 1056
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236 444 380 241 1223 746 782 1207
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242 496 391 195 1116 643 770 1219
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243 429 364 191 1118 694 783 1223
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244 410 371 236 1063 692 805 1233
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230 386 370 217 1087 657 787 1215
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275 404 402 214 1044 697 831 1188
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265 443 365 231 1086 694 782 1184
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255 390 354 246 1114 642 773 1176
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281 384 406 232 1102 719 787 1191
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263 459 369 251 1135 643 810 1215
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280 433 400 251 1159 701 777 1151
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278 385 382 231 1147 697 707 1161
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248 393 389 211 1162 723 759 1183
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251 403 385 246 1114 752 776 1153
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239 383 347 227 1172 759 789 1141
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We notice that the number of scales here is 4 because 16 = 2^4. Runnig the program on the above input file gives the following 3 output files:
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The first output file::
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motifs max_var at scale
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deletionHoptspot NA
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insertionHoptspot NA
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dnaPolPauseFrameshift NA
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indelHotspot NA
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topoisomeraseCleavageSite 3
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translinTarget NA
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vDjRecombinationSignal NA
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x.likeSite NA
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The second output file::
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motif 1_var 1_pval 1_test 2_var 2_pval 2_test 3_var 3_pval 3_test 4_var 4_pval 4_test
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deletionHoptspot 0.457 0.048 L 1.18 0.334 R 1.61 0.194 R 3.41 0.055 R
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insertionHoptspot 0.556 0.109 L 1.34 0.272 R 1.59 0.223 R 2.02 0.157 R
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dnaPolPauseFrameshift 1.42 0.089 R 0.66 0.331 L 0.421 0.305 L 0.121 0.268 L
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indelHotspot 0.373 0.021 L 1.36 0.254 R 1.24 0.301 R 4.09 0.047 R
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topoisomeraseCleavageSite 0.305 0.002 L 0.936 0.489 R 3.78 0.01 R 1.25 0.272 R
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translinTarget 0.525 0.061 L 1.69 0.11 R 2.02 0.131 R 0.00891 0.069 L
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vDjRecombinationSignal 0.68 0.138 L 0.957 0.46 R 2.35 0.071 R 1.03 0.357 R
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x.likeSite 0.928 0.402 L 1.33 0.261 R 0.735 0.431 L 0.783 0.422 R
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The third output file:
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.. image:: ./static/operation_icons/dwt_var_perClass.png
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</help>
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</tool>
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