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| date | Wed, 20 Jan 2016 09:10:43 -0500 |
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| 2 <head> | |
| 3 <title>MayaChemTools:Documentation:AnalyzeSDFilesData.pl</title> | |
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| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <div class="DocNav"> | |
| 14 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./README.html" title="README.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AnalyzeSequenceFilesData.html" title="AnalyzeSequenceFilesData.html">Next</a></td><td width="34%" align="middle"><strong>AnalyzeSDFilesData.pl</strong></td><td width="33%" align="right"><a href="././code/AnalyzeSDFilesData.html" title="View source code">Code</a> | <a href="./../pdf/AnalyzeSDFilesData.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/AnalyzeSDFilesData.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/AnalyzeSDFilesData.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/AnalyzeSDFilesData.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> | |
| 16 </table> | |
| 17 </div> | |
| 18 <p> | |
| 19 </p> | |
| 20 <h2>NAME</h2> | |
| 21 <p>AnalyzeSDFilesData.pl - Analyze numerical data field values in SDFile(s)</p> | |
| 22 <p> | |
| 23 </p> | |
| 24 <h2>SYNOPSIS</h2> | |
| 25 <p>AnalyzeSDFilesData.pl SDFile(s)...</p> | |
| 26 <p>AnalyzeSDFilesData.pl [<strong>--datafields</strong> "fieldlabel,[fieldlabel,...]" | All] | |
| 27 [<strong>--datafieldpairs</strong> "fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]" | AllPairs] [<strong>-d, --detail</strong> infolevel] | |
| 28 [<strong>-f, --fast</strong>] [<strong>--frequencybins</strong> number | "number,number,[number,...]"] | |
| 29 [<strong>-h, --help</strong>] [<strong>--klargest</strong> number] [<strong>--ksmallest</strong> number] | |
| 30 [<strong>-m, --mode</strong> DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | "function1, [function2,...]"] | |
| 31 [<strong>--trimfraction</strong> number] [<strong>-w, --workingdir</strong> dirname] SDFiles(s)...</p> | |
| 32 <p> | |
| 33 </p> | |
| 34 <h2>DESCRIPTION</h2> | |
| 35 <p>Analyze numerical data field values in <em>SDFile(s)</em> using a combination of various statistical | |
| 36 functions; Non-numerical values are simply ignored. For <em>Correlation, RSquare, and | |
| 37 Covariance</em> analysis, the count of valid values in specified data field pairs must be same; | |
| 38 otherwise, column data field pair is ignored. The file names are separated by space.The valid file | |
| 39 extensions are <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a | |
| 40 current directory can be specified either by <em>*.sdf</em> or the current directory name.</p> | |
| 41 <p> | |
| 42 </p> | |
| 43 <h2>OPTIONS</h2> | |
| 44 <dl> | |
| 45 <dt><strong><strong>--datafields</strong> <em>"fieldlabel,[fieldlabel,...]" | Common | All</em></strong></dt> | |
| 46 <dd> | |
| 47 <p>Data fields to use for analysis. Possible values: list of comma separated data field | |
| 48 labels, data fields common to all records, or all data fields. Default value: <em>Common</em>. | |
| 49 Examples:</p> | |
| 50 <div class="OptionsBox"> | |
| 51 ALogP,MolWeight,EC50 | |
| 52 <br/> "MolWeight,PSA"</div> | |
| 53 </dd> | |
| 54 <dt><strong><strong>--datafieldpairs</strong> <em>"fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]" | CommonPairs | AllPairs</em></strong></dt> | |
| 55 <dd> | |
| 56 <p>This value is mode specific and is only used for <em>Correlation, PearsonCorrelation, or | |
| 57 Covariance</em> value of <strong>-m, --mode</strong> option. It specifies data field label pairs to use | |
| 58 for data analysis during <em>Correlation</em> and <em>Covariance</em> calculations. Possible values: | |
| 59 comma delimited list of data field label pairs, data field label pairs common to all records, | |
| 60 or all data field pairs. Default value:<em>CommonPairs</em>. Example:</p> | |
| 61 <div class="OptionsBox"> | |
| 62 MolWeight,EC50,NumN+O,PSA</div> | |
| 63 <p>For <em>AllPairs</em> value of <strong>--datafieldpairs</strong> option, all data field label pairs are used for | |
| 64 <em>Correlation</em> and <em>Covariance</em> calculations.</p> | |
| 65 </dd> | |
| 66 <dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt> | |
| 67 <dd> | |
| 68 <p>Level of information to print about column values being ignored. Default: <em>0</em>. Possible values: | |
| 69 0, 1, 2, 3, or 4.</p> | |
| 70 </dd> | |
| 71 <dt><strong><strong>-f, --fast</strong></strong></dt> | |
| 72 <dd> | |
| 73 <p>In this mode, all the data field values specified for analysis are assumed to contain numerical | |
| 74 data and no checking is performed before analysis. By default, only numerical data is | |
| 75 used for analysis; other types of column data is ignored.</p> | |
| 76 </dd> | |
| 77 <dt><strong><strong>--frequencybins</strong> <em>number | "number,number,[number,...]"</em></strong></dt> | |
| 78 <dd> | |
| 79 <p>Specify number of bins or bin range to use for frequency analysis. Default value: <em>10</em></p> | |
| 80 <p>Number of bins value along with the smallest and largest value for a column is used to | |
| 81 group the column values into different groups.</p> | |
| 82 <p>The bin range list is used to group values for a column into different groups; It must contain | |
| 83 values in ascending order. Examples:</p> | |
| 84 <div class="OptionsBox"> | |
| 85 10,20,30 | |
| 86 <br/> 0.1,0.2,0.3,0.4,0.5</div> | |
| 87 <p>The frequency value calculated for a specific bin corresponds to all the column values | |
| 88 which are greater than the previous bin value and less than or equal to the current bin value.</p> | |
| 89 </dd> | |
| 90 <dt><strong><strong>-h, --help</strong></strong></dt> | |
| 91 <dd> | |
| 92 <p>Print this help message.</p> | |
| 93 </dd> | |
| 94 <dt><strong><strong>--klargest</strong> <em>number</em></strong></dt> | |
| 95 <dd> | |
| 96 <p>Kth largest value to find by <em>KLargest</em> function. Default value: <em>2</em>. Valid values: positive | |
| 97 integers.</p> | |
| 98 </dd> | |
| 99 <dt><strong><strong>--ksmallest</strong> <em>number</em></strong></dt> | |
| 100 <dd> | |
| 101 <p>Kth smallest value to find by <em>KSmallest</em> function. Default values: <em>2</em>. Valid values: positive | |
| 102 integers.</p> | |
| 103 </dd> | |
| 104 <dt><strong><strong>-m, --mode</strong> <em>DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | "function1, [function2,...]"</em></strong></dt> | |
| 105 <dd> | |
| 106 <p>Specify how to analyze data in SDFile(s): calculate basic or all descriptive statistics; or | |
| 107 use a comma delimited list of supported statistical functions. Possible values: | |
| 108 <em>DescriptiveStatisticsBasic | DescriptiveStatisticsAll | "function1,[function2]..."</em>. Default | |
| 109 value: <em>DescriptiveStatisticsBasic</em></p> | |
| 110 <p><em>DescriptiveStatisticsBasic</em> includes these functions: <em>Count, Maximum, Minimum, Mean, | |
| 111 Median, Sum, StandardDeviation, StandardError, Variance</em>.</p> | |
| 112 <p><em>DescriptiveStatisticsAll</em>, in addition to <em>DescriptiveStatisticsBasic</em> functions, includes: | |
| 113 <em>GeometricMean, Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, Mode, RSquare, | |
| 114 Skewness, TrimMean</em>.</p> | |
| 115 <p><em>All</em> uses complete list of supported functions: <em>Average, AverageDeviation, Correlation, | |
| 116 Count, Covariance, GeometricMean, Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, | |
| 117 Maximum, Minimum, Mean, Median, Mode, RSquare, Skewness, Sum, | |
| 118 SumOfSquares, StandardDeviation, StandardDeviationN, StandardError, StandardScores, | |
| 119 StandardScoresN, TrimMean, Variance, VarianceN</em>. The function names ending with N | |
| 120 calculate corresponding values assuming an entire population instead of a population sample. | |
| 121 Here are the formulas for these functions:</p> | |
| 122 <p>Average: See Mean</p> | |
| 123 <p>AverageDeviation: SUM( ABS(x[i] - Xmean) ) / n</p> | |
| 124 <p>Correlation: See Pearson Correlation</p> | |
| 125 <p>Covariance: SUM( (x[i] - Xmean)(y[i] - Ymean) ) / n</p> | |
| 126 <p>GeometricMean: NthROOT( PRODUCT(x[i]) )</p> | |
| 127 <p>HarmonicMean: 1 / ( SUM(1/x[i]) / n )</p> | |
| 128 <p>Mean: SUM( x[i] ) / n</p> | |
| 129 <p>Median: Xsorted[(n - 1)/2 + 1] for even values of n; (Xsorted[n/2] + Xsorted[n/2 + 1])/2 | |
| 130 for odd values of n.</p> | |
| 131 <p>Kurtosis: [ {n(n + 1)/(n - 1)(n - 2)(n - 3)} SUM{ ((x[i] - Xmean)/STDDEV)^4 } ] - | |
| 132 {3((n - 1)^2)}/{(n - 2)(n-3)}</p> | |
| 133 <p>PearsonCorrelation: SUM( (x[i] - Xmean)(y[i] - Ymean) ) / SQRT( SUM( (x[i] - Xmean)^2 ) | |
| 134 (SUM( (y[i] - Ymean)^2 )) )</p> | |
| 135 <p>RSquare: PearsonCorrelation^2</p> | |
| 136 <p>Skewness: {n/(n - 1)(n - 2)} SUM{ ((x[i] - Xmean)/STDDEV)^3 }</p> | |
| 137 <p>StandardDeviation: SQRT ( SUM( (x[i] - Mean)^2 ) / (n - 1) )</p> | |
| 138 <p>StandardDeviationN: SQRT ( SUM( (x[i] - Mean)^2 ) / n )</p> | |
| 139 <p>StandardError: StandardDeviation / SQRT( n )</p> | |
| 140 <p>StandardScore: (x[i] - Mean) / (n - 1)</p> | |
| 141 <p>StandardScoreN: (x[i] - Mean) / n</p> | |
| 142 <p>Variance: SUM( (x[i] - Xmean)^2 / (n - 1) )</p> | |
| 143 <p>VarianceN: SUM( (x[i] - Xmean)^2 / n )</p> | |
| 144 </dd> | |
| 145 <dt><strong><strong>-o, --overwrite</strong></strong></dt> | |
| 146 <dd> | |
| 147 <p>Overwrite existing files.</p> | |
| 148 </dd> | |
| 149 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt> | |
| 150 <dd> | |
| 151 <p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em> | |
| 152 Default value: <em>comma</em>.</p> | |
| 153 </dd> | |
| 154 <dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt> | |
| 155 <dd> | |
| 156 <p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places. | |
| 157 Valid values: positive integers.</p> | |
| 158 </dd> | |
| 159 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt> | |
| 160 <dd> | |
| 161 <p>Put quotes around column values in output text file. Possible values: <em>yes or | |
| 162 no</em>. Default value: <em>yes</em>.</p> | |
| 163 </dd> | |
| 164 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> | |
| 165 <dd> | |
| 166 <p>New text file name is generated using the root: <Root>.<Ext>. Default new file | |
| 167 name: <InitialSDFileName><Mode>.<Ext>. Based on the specified analysis, | |
| 168 <Mode> corresponds to one of these values: DescriptiveStatisticsBasic, | |
| 169 DescriptiveStatisticsAll, AllStatistics, SpecifiedStatistics, Covariance, Correlation, | |
| 170 Frequency, or StandardScores. The csv, and tsv <Ext> values are used for | |
| 171 comma/semicolon, and tab delimited text files respectively. This option is ignored for | |
| 172 multiple input files.</p> | |
| 173 </dd> | |
| 174 <dt><strong><strong>--trimfraction</strong> <em>number</em></strong></dt> | |
| 175 <dd> | |
| 176 <p>Fraction of data to exclude from the top and bottom of the data set during | |
| 177 <em>TrimMean</em> calculation. Default value: <em>0.1</em> Valid values: > 0 and < 1.</p> | |
| 178 </dd> | |
| 179 <dt><strong><strong>-w --workingdir</strong> <em>text</em></strong></dt> | |
| 180 <dd> | |
| 181 <p>Location of working directory. Default: current directory.</p> | |
| 182 </dd> | |
| 183 </dl> | |
| 184 <p> | |
| 185 </p> | |
| 186 <h2>EXAMPLES</h2> | |
| 187 <p>To calculate basic statistics for data in all common data fields and generate a | |
| 188 NewSample1DescriptiveStatisticsBasic.csv file, type:</p> | |
| 189 <div class="ExampleBox"> | |
| 190 % AnalyzeSDFilesData.pl -o -r NewSample1 Sample1.sdf</div> | |
| 191 <p>To calculate basic statistics for MolWeight data field and generate a | |
| 192 NewSample1DescriptiveStatisticsBasic.csv file, type:</p> | |
| 193 <div class="ExampleBox"> | |
| 194 % AnalyzeSDFilesData.pl --datafields MolWeight -o -r NewSample1 | |
| 195 Sample1.sdf</div> | |
| 196 <p>To calculate all available statistics for MolWeight data field and all data field pairs, | |
| 197 and generate NewSample1DescriptiveStatisticsAll.csv, NewSample1CorrelationMatrix.csv, | |
| 198 NewSample1CorrelationMatrix.csv, and NewSample1MolWeightFrequencyAnalysis.csv | |
| 199 files, type:</p> | |
| 200 <div class="ExampleBox"> | |
| 201 % AnalyzeSDFilesData.pl -m DescriptiveStatisticsAll --datafields | |
| 202 MolWeight -o --datafieldpairs AllPairs -r NewSample1 Sample1.sdf</div> | |
| 203 <p>To compute frequency distribution of MolWeight data field into five bins and | |
| 204 generate NewSample1MolWeightFrequencyAnalysis.csv, type:</p> | |
| 205 <div class="ExampleBox"> | |
| 206 % AnalyzeSDFilesData.pl -m Frequency --frequencybins 5 --datafields | |
| 207 MolWeight -o -r NewSample1 Sample1.sdf</div> | |
| 208 <p>To compute frequency distribution of data in MolWeight data field into specified bin range | |
| 209 values, and generate NewSample1MolWeightFrequencyAnalysis.csv, type:</p> | |
| 210 <div class="ExampleBox"> | |
| 211 % AnalyzeSDFilesData.pl -m Frequency --frequencybins "100,200,400" | |
| 212 --datafields MolWeight -o -r NewSample1 Sample1.sdf</div> | |
| 213 <p>To calculate all available statistics for data in all data fields and pairs, type:</p> | |
| 214 <div class="ExampleBox"> | |
| 215 % AnalyzeSDFilesData.pl -m All --datafields All --datafieldpairs | |
| 216 AllPairs -o -r NewSample1 Sample1.sdf</div> | |
| 217 <p> | |
| 218 </p> | |
| 219 <h2>AUTHOR</h2> | |
| 220 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> | |
| 221 <p> | |
| 222 </p> | |
| 223 <h2>SEE ALSO</h2> | |
| 224 <p><a href="./FilterSDFiles.html">FilterSDFiles.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./SplitSDFiles.html">SplitSDFiles.pl</a>, <a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.pl</a> | |
| 225 </p> | |
| 226 <p> | |
| 227 </p> | |
| 228 <h2>COPYRIGHT</h2> | |
| 229 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> | |
| 230 <p>This file is part of MayaChemTools.</p> | |
| 231 <p>MayaChemTools is free software; you can redistribute it and/or modify it under | |
| 232 the terms of the GNU Lesser General Public License as published by the Free | |
| 233 Software Foundation; either version 3 of the License, or (at your option) | |
| 234 any later version.</p> | |
| 235 <p> </p><p> </p><div class="DocNav"> | |
| 236 <table width="100%" border=0 cellpadding=0 cellspacing=2> | |
| 237 <tr align="left" valign="top"><td width="33%" align="left"><a href="./README.html" title="README.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AnalyzeSequenceFilesData.html" title="AnalyzeSequenceFilesData.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>AnalyzeSDFilesData.pl</strong></td></tr> | |
| 238 </table> | |
| 239 </div> | |
| 240 <br /> | |
| 241 <center> | |
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| 245 </html> |