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124 .\" ======================================================================== | |
125 .\" | |
126 .IX Title "ANALYZESDFILESDATA 1" | |
127 .TH ANALYZESDFILESDATA 1 "2015-03-29" "perl v5.14.2" "MayaChemTools" | |
128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes | |
129 .\" way too many mistakes in technical documents. | |
130 .if n .ad l | |
131 .nh | |
132 .SH "NAME" | |
133 AnalyzeSDFilesData.pl \- Analyze numerical data field values in SDFile(s) | |
134 .SH "SYNOPSIS" | |
135 .IX Header "SYNOPSIS" | |
136 AnalyzeSDFilesData.pl SDFile(s)... | |
137 .PP | |
138 AnalyzeSDFilesData.pl [\fB\-\-datafields\fR \*(L"fieldlabel,[fieldlabel,...]\*(R" | All] | |
139 [\fB\-\-datafieldpairs\fR \*(L"fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]\*(R" | AllPairs] [\fB\-d, \-\-detail\fR infolevel] | |
140 [\fB\-f, \-\-fast\fR] [\fB\-\-frequencybins\fR number | \*(L"number,number,[number,...]\*(R"] | |
141 [\fB\-h, \-\-help\fR] [\fB\-\-klargest\fR number] [\fB\-\-ksmallest\fR number] | |
142 [\fB\-m, \-\-mode\fR DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | \*(L"function1, [function2,...]\*(R"] | |
143 [\fB\-\-trimfraction\fR number] [\fB\-w, \-\-workingdir\fR dirname] SDFiles(s)... | |
144 .SH "DESCRIPTION" | |
145 .IX Header "DESCRIPTION" | |
146 Analyze numerical data field values in \fISDFile(s)\fR using a combination of various statistical | |
147 functions; Non-numerical values are simply ignored. For \fICorrelation, RSquare, and | |
148 Covariance\fR analysis, the count of valid values in specified data field pairs must be same; | |
149 otherwise, column data field pair is ignored. The file names are separated by space.The valid file | |
150 extensions are \fI.sdf\fR and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a | |
151 current directory can be specified either by \fI*.sdf\fR or the current directory name. | |
152 .SH "OPTIONS" | |
153 .IX Header "OPTIONS" | |
154 .ie n .IP "\fB\-\-datafields\fR \fI""fieldlabel,[fieldlabel,...]"" | Common | All\fR" 4 | |
155 .el .IP "\fB\-\-datafields\fR \fI``fieldlabel,[fieldlabel,...]'' | Common | All\fR" 4 | |
156 .IX Item "--datafields fieldlabel,[fieldlabel,...] | Common | All" | |
157 Data fields to use for analysis. Possible values: list of comma separated data field | |
158 labels, data fields common to all records, or all data fields. Default value: \fICommon\fR. | |
159 Examples: | |
160 .Sp | |
161 .Vb 2 | |
162 \& ALogP,MolWeight,EC50 | |
163 \& "MolWeight,PSA" | |
164 .Ve | |
165 .ie n .IP "\fB\-\-datafieldpairs\fR \fI""fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]"" | CommonPairs | AllPairs\fR" 4 | |
166 .el .IP "\fB\-\-datafieldpairs\fR \fI``fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]'' | CommonPairs | AllPairs\fR" 4 | |
167 .IX Item "--datafieldpairs fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...] | CommonPairs | AllPairs" | |
168 This value is mode specific and is only used for \fICorrelation, PearsonCorrelation, or | |
169 Covariance\fR value of \fB\-m, \-\-mode\fR option. It specifies data field label pairs to use | |
170 for data analysis during \fICorrelation\fR and \fICovariance\fR calculations. Possible values: | |
171 comma delimited list of data field label pairs, data field label pairs common to all records, | |
172 or all data field pairs. Default value:\fICommonPairs\fR. Example: | |
173 .Sp | |
174 .Vb 1 | |
175 \& MolWeight,EC50,NumN+O,PSA | |
176 .Ve | |
177 .Sp | |
178 For \fIAllPairs\fR value of \fB\-\-datafieldpairs\fR option, all data field label pairs are used for | |
179 \&\fICorrelation\fR and \fICovariance\fR calculations. | |
180 .IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4 | |
181 .IX Item "-d, --detail infolevel" | |
182 Level of information to print about column values being ignored. Default: \fI0\fR. Possible values: | |
183 0, 1, 2, 3, or 4. | |
184 .IP "\fB\-f, \-\-fast\fR" 4 | |
185 .IX Item "-f, --fast" | |
186 In this mode, all the data field values specified for analysis are assumed to contain numerical | |
187 data and no checking is performed before analysis. By default, only numerical data is | |
188 used for analysis; other types of column data is ignored. | |
189 .ie n .IP "\fB\-\-frequencybins\fR \fInumber | ""number,number,[number,...]""\fR" 4 | |
190 .el .IP "\fB\-\-frequencybins\fR \fInumber | ``number,number,[number,...]''\fR" 4 | |
191 .IX Item "--frequencybins number | number,number,[number,...]" | |
192 Specify number of bins or bin range to use for frequency analysis. Default value: \fI10\fR | |
193 .Sp | |
194 Number of bins value along with the smallest and largest value for a column is used to | |
195 group the column values into different groups. | |
196 .Sp | |
197 The bin range list is used to group values for a column into different groups; It must contain | |
198 values in ascending order. Examples: | |
199 .Sp | |
200 .Vb 2 | |
201 \& 10,20,30 | |
202 \& 0.1,0.2,0.3,0.4,0.5 | |
203 .Ve | |
204 .Sp | |
205 The frequency value calculated for a specific bin corresponds to all the column values | |
206 which are greater than the previous bin value and less than or equal to the current bin value. | |
207 .IP "\fB\-h, \-\-help\fR" 4 | |
208 .IX Item "-h, --help" | |
209 Print this help message. | |
210 .IP "\fB\-\-klargest\fR \fInumber\fR" 4 | |
211 .IX Item "--klargest number" | |
212 Kth largest value to find by \fIKLargest\fR function. Default value: \fI2\fR. Valid values: positive | |
213 integers. | |
214 .IP "\fB\-\-ksmallest\fR \fInumber\fR" 4 | |
215 .IX Item "--ksmallest number" | |
216 Kth smallest value to find by \fIKSmallest\fR function. Default values: \fI2\fR. Valid values: positive | |
217 integers. | |
218 .ie n .IP "\fB\-m, \-\-mode\fR \fIDescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | ""function1, [function2,...]""\fR" 4 | |
219 .el .IP "\fB\-m, \-\-mode\fR \fIDescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | ``function1, [function2,...]''\fR" 4 | |
220 .IX Item "-m, --mode DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | function1, [function2,...]" | |
221 Specify how to analyze data in SDFile(s): calculate basic or all descriptive statistics; or | |
222 use a comma delimited list of supported statistical functions. Possible values: | |
223 \&\fIDescriptiveStatisticsBasic | DescriptiveStatisticsAll | \*(L"function1,[function2]...\*(R"\fR. Default | |
224 value: \fIDescriptiveStatisticsBasic\fR | |
225 .Sp | |
226 \&\fIDescriptiveStatisticsBasic\fR includes these functions: \fICount, Maximum, Minimum, Mean, | |
227 Median, Sum, StandardDeviation, StandardError, Variance\fR. | |
228 .Sp | |
229 \&\fIDescriptiveStatisticsAll\fR, in addition to \fIDescriptiveStatisticsBasic\fR functions, includes: | |
230 \&\fIGeometricMean, Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, Mode, RSquare, | |
231 Skewness, TrimMean\fR. | |
232 .Sp | |
233 \&\fIAll\fR uses complete list of supported functions: \fIAverage, AverageDeviation, Correlation, | |
234 Count, Covariance, GeometricMean, Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, | |
235 Maximum, Minimum, Mean, Median, Mode, RSquare, Skewness, Sum, | |
236 SumOfSquares, StandardDeviation, StandardDeviationN, StandardError, StandardScores, | |
237 StandardScoresN, TrimMean, Variance, VarianceN\fR. The function names ending with N | |
238 calculate corresponding values assuming an entire population instead of a population sample. | |
239 Here are the formulas for these functions: | |
240 .Sp | |
241 Average: See Mean | |
242 .Sp | |
243 AverageDeviation: \s-1SUM\s0( \s-1ABS\s0(x[i] \- Xmean) ) / n | |
244 .Sp | |
245 Correlation: See Pearson Correlation | |
246 .Sp | |
247 Covariance: \s-1SUM\s0( (x[i] \- Xmean)(y[i] \- Ymean) ) / n | |
248 .Sp | |
249 GeometricMean: NthROOT( \s-1PRODUCT\s0(x[i]) ) | |
250 .Sp | |
251 HarmonicMean: 1 / ( \s-1SUM\s0(1/x[i]) / n ) | |
252 .Sp | |
253 Mean: \s-1SUM\s0( x[i] ) / n | |
254 .Sp | |
255 Median: Xsorted[(n \- 1)/2 + 1] for even values of n; (Xsorted[n/2] + Xsorted[n/2 + 1])/2 | |
256 for odd values of n. | |
257 .Sp | |
258 Kurtosis: [ {n(n + 1)/(n \- 1)(n \- 2)(n \- 3)} SUM{ ((x[i] \- Xmean)/STDDEV)^4 } ] \- | |
259 {3((n \- 1)^2)}/{(n \- 2)(n\-3)} | |
260 .Sp | |
261 PearsonCorrelation: \s-1SUM\s0( (x[i] \- Xmean)(y[i] \- Ymean) ) / \s-1SQRT\s0( \s-1SUM\s0( (x[i] \- Xmean)^2 ) | |
262 (\s-1SUM\s0( (y[i] \- Ymean)^2 )) ) | |
263 .Sp | |
264 RSquare: PearsonCorrelation^2 | |
265 .Sp | |
266 Skewness: {n/(n \- 1)(n \- 2)} SUM{ ((x[i] \- Xmean)/STDDEV)^3 } | |
267 .Sp | |
268 StandardDeviation: \s-1SQRT\s0 ( \s-1SUM\s0( (x[i] \- Mean)^2 ) / (n \- 1) ) | |
269 .Sp | |
270 StandardDeviationN: \s-1SQRT\s0 ( \s-1SUM\s0( (x[i] \- Mean)^2 ) / n ) | |
271 .Sp | |
272 StandardError: StandardDeviation / \s-1SQRT\s0( n ) | |
273 .Sp | |
274 StandardScore: (x[i] \- Mean) / (n \- 1) | |
275 .Sp | |
276 StandardScoreN: (x[i] \- Mean) / n | |
277 .Sp | |
278 Variance: \s-1SUM\s0( (x[i] \- Xmean)^2 / (n \- 1) ) | |
279 .Sp | |
280 VarianceN: \s-1SUM\s0( (x[i] \- Xmean)^2 / n ) | |
281 .IP "\fB\-o, \-\-overwrite\fR" 4 | |
282 .IX Item "-o, --overwrite" | |
283 Overwrite existing files. | |
284 .IP "\fB\-\-outdelim\fR \fIcomma | tab | semicolon\fR" 4 | |
285 .IX Item "--outdelim comma | tab | semicolon" | |
286 Output text file delimiter. Possible values: \fIcomma, tab, or semicolon\fR | |
287 Default value: \fIcomma\fR. | |
288 .IP "\fB\-p, \-\-precision\fR \fInumber\fR" 4 | |
289 .IX Item "-p, --precision number" | |
290 Precision of calculated values in the output file. Default: up to \fI2\fR decimal places. | |
291 Valid values: positive integers. | |
292 .IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4 | |
293 .IX Item "-q, --quote yes | no" | |
294 Put quotes around column values in output text file. Possible values: \fIyes or | |
295 no\fR. Default value: \fIyes\fR. | |
296 .IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 | |
297 .IX Item "-r, --root rootname" | |
298 New text file name is generated using the root: <Root>.<Ext>. Default new file | |
299 name: <InitialSDFileName><Mode>.<Ext>. Based on the specified analysis, | |
300 <Mode> corresponds to one of these values: DescriptiveStatisticsBasic, | |
301 DescriptiveStatisticsAll, AllStatistics, SpecifiedStatistics, Covariance, Correlation, | |
302 Frequency, or StandardScores. The csv, and tsv <Ext> values are used for | |
303 comma/semicolon, and tab delimited text files respectively. This option is ignored for | |
304 multiple input files. | |
305 .IP "\fB\-\-trimfraction\fR \fInumber\fR" 4 | |
306 .IX Item "--trimfraction number" | |
307 Fraction of data to exclude from the top and bottom of the data set during | |
308 \&\fITrimMean\fR calculation. Default value: \fI0.1\fR Valid values: > 0 and < 1. | |
309 .IP "\fB\-w \-\-workingdir\fR \fItext\fR" 4 | |
310 .IX Item "-w --workingdir text" | |
311 Location of working directory. Default: current directory. | |
312 .SH "EXAMPLES" | |
313 .IX Header "EXAMPLES" | |
314 To calculate basic statistics for data in all common data fields and generate a | |
315 NewSample1DescriptiveStatisticsBasic.csv file, type: | |
316 .PP | |
317 .Vb 1 | |
318 \& % AnalyzeSDFilesData.pl \-o \-r NewSample1 Sample1.sdf | |
319 .Ve | |
320 .PP | |
321 To calculate basic statistics for MolWeight data field and generate a | |
322 NewSample1DescriptiveStatisticsBasic.csv file, type: | |
323 .PP | |
324 .Vb 2 | |
325 \& % AnalyzeSDFilesData.pl \-\-datafields MolWeight \-o \-r NewSample1 | |
326 \& Sample1.sdf | |
327 .Ve | |
328 .PP | |
329 To calculate all available statistics for MolWeight data field and all data field pairs, | |
330 and generate NewSample1DescriptiveStatisticsAll.csv, NewSample1CorrelationMatrix.csv, | |
331 NewSample1CorrelationMatrix.csv, and NewSample1MolWeightFrequencyAnalysis.csv | |
332 files, type: | |
333 .PP | |
334 .Vb 2 | |
335 \& % AnalyzeSDFilesData.pl \-m DescriptiveStatisticsAll \-\-datafields | |
336 \& MolWeight \-o \-\-datafieldpairs AllPairs \-r NewSample1 Sample1.sdf | |
337 .Ve | |
338 .PP | |
339 To compute frequency distribution of MolWeight data field into five bins and | |
340 generate NewSample1MolWeightFrequencyAnalysis.csv, type: | |
341 .PP | |
342 .Vb 2 | |
343 \& % AnalyzeSDFilesData.pl \-m Frequency \-\-frequencybins 5 \-\-datafields | |
344 \& MolWeight \-o \-r NewSample1 Sample1.sdf | |
345 .Ve | |
346 .PP | |
347 To compute frequency distribution of data in MolWeight data field into specified bin range | |
348 values, and generate NewSample1MolWeightFrequencyAnalysis.csv, type: | |
349 .PP | |
350 .Vb 2 | |
351 \& % AnalyzeSDFilesData.pl \-m Frequency \-\-frequencybins "100,200,400" | |
352 \& \-\-datafields MolWeight \-o \-r NewSample1 Sample1.sdf | |
353 .Ve | |
354 .PP | |
355 To calculate all available statistics for data in all data fields and pairs, type: | |
356 .PP | |
357 .Vb 2 | |
358 \& % AnalyzeSDFilesData.pl \-m All \-\-datafields All \-\-datafieldpairs | |
359 \& AllPairs \-o \-r NewSample1 Sample1.sdf | |
360 .Ve | |
361 .SH "AUTHOR" | |
362 .IX Header "AUTHOR" | |
363 Manish Sud <msud@san.rr.com> | |
364 .SH "SEE ALSO" | |
365 .IX Header "SEE ALSO" | |
366 FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, MergeTextFilesWithSD.pl | |
367 .SH "COPYRIGHT" | |
368 .IX Header "COPYRIGHT" | |
369 Copyright (C) 2015 Manish Sud. All rights reserved. | |
370 .PP | |
371 This file is part of MayaChemTools. | |
372 .PP | |
373 MayaChemTools is free software; you can redistribute it and/or modify it under | |
374 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free | |
375 Software Foundation; either version 3 of the License, or (at your option) | |
376 any later version. |