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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/AnalyzeSDFilesData.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,245 @@ +<html> +<head> +<title>MayaChemTools:Documentation:AnalyzeSDFilesData.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>AnalyzeSDFilesData.pl - Analyze numerical data field values in SDFile(s)</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>AnalyzeSDFilesData.pl SDFile(s)...</p> +<p>AnalyzeSDFilesData.pl [<strong>--datafields</strong> "fieldlabel,[fieldlabel,...]" | All] +[<strong>--datafieldpairs</strong> "fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]" | AllPairs] [<strong>-d, --detail</strong> infolevel] +[<strong>-f, --fast</strong>] [<strong>--frequencybins</strong> number | "number,number,[number,...]"] +[<strong>-h, --help</strong>] [<strong>--klargest</strong> number] [<strong>--ksmallest</strong> number] +[<strong>-m, --mode</strong> DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | "function1, [function2,...]"] +[<strong>--trimfraction</strong> number] [<strong>-w, --workingdir</strong> dirname] SDFiles(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Analyze numerical data field values in <em>SDFile(s)</em> using a combination of various statistical +functions; Non-numerical values are simply ignored. For <em>Correlation, RSquare, and +Covariance</em> analysis, the count of valid values in specified data field pairs must be same; +otherwise, column data field pair is ignored. The file names are separated by space.The valid file +extensions are <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a +current directory can be specified either by <em>*.sdf</em> or the current directory name.</p> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>--datafields</strong> <em>"fieldlabel,[fieldlabel,...]" | Common | All</em></strong></dt> +<dd> +<p>Data fields to use for analysis. Possible values: list of comma separated data field +labels, data fields common to all records, or all data fields. Default value: <em>Common</em>. +Examples:</p> +<div class="OptionsBox"> + ALogP,MolWeight,EC50 +<br/> "MolWeight,PSA"</div> +</dd> +<dt><strong><strong>--datafieldpairs</strong> <em>"fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]" | CommonPairs | AllPairs</em></strong></dt> +<dd> +<p>This value is mode specific and is only used for <em>Correlation, PearsonCorrelation, or +Covariance</em> value of <strong>-m, --mode</strong> option. It specifies data field label pairs to use +for data analysis during <em>Correlation</em> and <em>Covariance</em> calculations. Possible values: +comma delimited list of data field label pairs, data field label pairs common to all records, +or all data field pairs. Default value:<em>CommonPairs</em>. Example:</p> +<div class="OptionsBox"> + MolWeight,EC50,NumN+O,PSA</div> +<p>For <em>AllPairs</em> value of <strong>--datafieldpairs</strong> option, all data field label pairs are used for +<em>Correlation</em> and <em>Covariance</em> calculations.</p> +</dd> +<dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt> +<dd> +<p>Level of information to print about column values being ignored. Default: <em>0</em>. Possible values: +0, 1, 2, 3, or 4.</p> +</dd> +<dt><strong><strong>-f, --fast</strong></strong></dt> +<dd> +<p>In this mode, all the data field values specified for analysis are assumed to contain numerical +data and no checking is performed before analysis. By default, only numerical data is +used for analysis; other types of column data is ignored.</p> +</dd> +<dt><strong><strong>--frequencybins</strong> <em>number | "number,number,[number,...]"</em></strong></dt> +<dd> +<p>Specify number of bins or bin range to use for frequency analysis. Default value: <em>10</em></p> +<p>Number of bins value along with the smallest and largest value for a column is used to +group the column values into different groups.</p> +<p>The bin range list is used to group values for a column into different groups; It must contain +values in ascending order. Examples:</p> +<div class="OptionsBox"> + 10,20,30 +<br/> 0.1,0.2,0.3,0.4,0.5</div> +<p>The frequency value calculated for a specific bin corresponds to all the column values +which are greater than the previous bin value and less than or equal to the current bin value.</p> +</dd> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>--klargest</strong> <em>number</em></strong></dt> +<dd> +<p>Kth largest value to find by <em>KLargest</em> function. Default value: <em>2</em>. Valid values: positive +integers.</p> +</dd> +<dt><strong><strong>--ksmallest</strong> <em>number</em></strong></dt> +<dd> +<p>Kth smallest value to find by <em>KSmallest</em> function. Default values: <em>2</em>. Valid values: positive +integers.</p> +</dd> +<dt><strong><strong>-m, --mode</strong> <em>DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All | "function1, [function2,...]"</em></strong></dt> +<dd> +<p>Specify how to analyze data in SDFile(s): calculate basic or all descriptive statistics; or +use a comma delimited list of supported statistical functions. Possible values: +<em>DescriptiveStatisticsBasic | DescriptiveStatisticsAll | "function1,[function2]..."</em>. Default +value: <em>DescriptiveStatisticsBasic</em></p> +<p><em>DescriptiveStatisticsBasic</em> includes these functions: <em>Count, Maximum, Minimum, Mean, +Median, Sum, StandardDeviation, StandardError, Variance</em>.</p> +<p><em>DescriptiveStatisticsAll</em>, in addition to <em>DescriptiveStatisticsBasic</em> functions, includes: +<em>GeometricMean, Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, Mode, RSquare, +Skewness, TrimMean</em>.</p> +<p><em>All</em> uses complete list of supported functions: <em>Average, AverageDeviation, Correlation, +Count, Covariance, GeometricMean, Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, +Maximum, Minimum, Mean, Median, Mode, RSquare, Skewness, Sum, +SumOfSquares, StandardDeviation, StandardDeviationN, StandardError, StandardScores, +StandardScoresN, TrimMean, Variance, VarianceN</em>. The function names ending with N +calculate corresponding values assuming an entire population instead of a population sample. +Here are the formulas for these functions:</p> +<p>Average: See Mean</p> +<p>AverageDeviation: SUM( ABS(x[i] - Xmean) ) / n</p> +<p>Correlation: See Pearson Correlation</p> +<p>Covariance: SUM( (x[i] - Xmean)(y[i] - Ymean) ) / n</p> +<p>GeometricMean: NthROOT( PRODUCT(x[i]) )</p> +<p>HarmonicMean: 1 / ( SUM(1/x[i]) / n )</p> +<p>Mean: SUM( x[i] ) / n</p> +<p>Median: Xsorted[(n - 1)/2 + 1] for even values of n; (Xsorted[n/2] + Xsorted[n/2 + 1])/2 +for odd values of n.</p> +<p>Kurtosis: [ {n(n + 1)/(n - 1)(n - 2)(n - 3)} SUM{ ((x[i] - Xmean)/STDDEV)^4 } ] - +{3((n - 1)^2)}/{(n - 2)(n-3)}</p> +<p>PearsonCorrelation: SUM( (x[i] - Xmean)(y[i] - Ymean) ) / SQRT( SUM( (x[i] - Xmean)^2 ) +(SUM( (y[i] - Ymean)^2 )) )</p> +<p>RSquare: PearsonCorrelation^2</p> +<p>Skewness: {n/(n - 1)(n - 2)} SUM{ ((x[i] - Xmean)/STDDEV)^3 }</p> +<p>StandardDeviation: SQRT ( SUM( (x[i] - Mean)^2 ) / (n - 1) )</p> +<p>StandardDeviationN: SQRT ( SUM( (x[i] - Mean)^2 ) / n )</p> +<p>StandardError: StandardDeviation / SQRT( n )</p> +<p>StandardScore: (x[i] - Mean) / (n - 1)</p> +<p>StandardScoreN: (x[i] - Mean) / n</p> +<p>Variance: SUM( (x[i] - Xmean)^2 / (n - 1) )</p> +<p>VarianceN: SUM( (x[i] - Xmean)^2 / n )</p> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files.</p> +</dd> +<dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt> +<dd> +<p>Output text file delimiter. Possible values: <em>comma, tab, or semicolon</em> +Default value: <em>comma</em>.</p> +</dd> +<dt><strong><strong>-p, --precision</strong> <em>number</em></strong></dt> +<dd> +<p>Precision of calculated values in the output file. Default: up to <em>2</em> decimal places. +Valid values: positive integers.</p> +</dd> +<dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt> +<dd> +<p>Put quotes around column values in output text file. Possible values: <em>yes or +no</em>. Default value: <em>yes</em>.</p> +</dd> +<dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> +<dd> +<p>New text file name is generated using the root: <Root>.<Ext>. Default new file +name: <InitialSDFileName><Mode>.<Ext>. Based on the specified analysis, +<Mode> corresponds to one of these values: DescriptiveStatisticsBasic, +DescriptiveStatisticsAll, AllStatistics, SpecifiedStatistics, Covariance, Correlation, +Frequency, or StandardScores. The csv, and tsv <Ext> values are used for +comma/semicolon, and tab delimited text files respectively. This option is ignored for +multiple input files.</p> +</dd> +<dt><strong><strong>--trimfraction</strong> <em>number</em></strong></dt> +<dd> +<p>Fraction of data to exclude from the top and bottom of the data set during +<em>TrimMean</em> calculation. Default value: <em>0.1</em> Valid values: > 0 and < 1.</p> +</dd> +<dt><strong><strong>-w --workingdir</strong> <em>text</em></strong></dt> +<dd> +<p>Location of working directory. Default: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To calculate basic statistics for data in all common data fields and generate a +NewSample1DescriptiveStatisticsBasic.csv file, type:</p> +<div class="ExampleBox"> + % AnalyzeSDFilesData.pl -o -r NewSample1 Sample1.sdf</div> +<p>To calculate basic statistics for MolWeight data field and generate a +NewSample1DescriptiveStatisticsBasic.csv file, type:</p> +<div class="ExampleBox"> + % AnalyzeSDFilesData.pl --datafields MolWeight -o -r NewSample1 + Sample1.sdf</div> +<p>To calculate all available statistics for MolWeight data field and all data field pairs, +and generate NewSample1DescriptiveStatisticsAll.csv, NewSample1CorrelationMatrix.csv, +NewSample1CorrelationMatrix.csv, and NewSample1MolWeightFrequencyAnalysis.csv +files, type:</p> +<div class="ExampleBox"> + % AnalyzeSDFilesData.pl -m DescriptiveStatisticsAll --datafields + MolWeight -o --datafieldpairs AllPairs -r NewSample1 Sample1.sdf</div> +<p>To compute frequency distribution of MolWeight data field into five bins and +generate NewSample1MolWeightFrequencyAnalysis.csv, type:</p> +<div class="ExampleBox"> + % AnalyzeSDFilesData.pl -m Frequency --frequencybins 5 --datafields + MolWeight -o -r NewSample1 Sample1.sdf</div> +<p>To compute frequency distribution of data in MolWeight data field into specified bin range +values, and generate NewSample1MolWeightFrequencyAnalysis.csv, type:</p> +<div class="ExampleBox"> + % AnalyzeSDFilesData.pl -m Frequency --frequencybins "100,200,400" + --datafields MolWeight -o -r NewSample1 Sample1.sdf</div> +<p>To calculate all available statistics for data in all data fields and pairs, type:</p> +<div class="ExampleBox"> + % AnalyzeSDFilesData.pl -m All --datafields All --datafieldpairs + AllPairs -o -r NewSample1 Sample1.sdf</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<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> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>