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diff docs/scripts/txt/AnalyzeSDFilesData.txt @ 0:4816e4a8ae95 draft default tip
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author | deepakjadmin |
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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/txt/AnalyzeSDFilesData.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,245 @@ +NAME + AnalyzeSDFilesData.pl - Analyze numerical data field values in SDFile(s) + +SYNOPSIS + AnalyzeSDFilesData.pl SDFile(s)... + + AnalyzeSDFilesData.pl [--datafields "fieldlabel,[fieldlabel,...]" | All] + [--datafieldpairs "fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]" | + AllPairs] [-d, --detail infolevel] [-f, --fast] [--frequencybins number + | "number,number,[number,...]"] [-h, --help] [--klargest number] + [--ksmallest number] [-m, --mode DescriptiveStatisticsBasic | + DescriptiveStatisticsAll | All | "function1, [function2,...]"] + [--trimfraction number] [-w, --workingdir dirname] SDFiles(s)... + +DESCRIPTION + Analyze numerical data field values in *SDFile(s)* using a combination + of various statistical functions; Non-numerical values are simply + ignored. For *Correlation, RSquare, and Covariance* 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 *.sdf* and *.sd*. All other file + names are ignored. All the SD files in a current directory can be + specified either by **.sdf* or the current directory name. + +OPTIONS + --datafields *"fieldlabel,[fieldlabel,...]" | Common | All* + 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: *Common*. Examples: + + ALogP,MolWeight,EC50 + "MolWeight,PSA" + + --datafieldpairs *"fieldlabel,fieldlabel,[fieldlabel,fieldlabel,...]" | + CommonPairs | AllPairs* + This value is mode specific and is only used for *Correlation, + PearsonCorrelation, or Covariance* value of -m, --mode option. It + specifies data field label pairs to use for data analysis during + *Correlation* and *Covariance* 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:*CommonPairs*. Example: + + MolWeight,EC50,NumN+O,PSA + + For *AllPairs* value of --datafieldpairs option, all data field + label pairs are used for *Correlation* and *Covariance* + calculations. + + -d, --detail *infolevel* + Level of information to print about column values being ignored. + Default: *0*. Possible values: 0, 1, 2, 3, or 4. + + -f, --fast + 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. + + --frequencybins *number | "number,number,[number,...]"* + Specify number of bins or bin range to use for frequency analysis. + Default value: *10* + + Number of bins value along with the smallest and largest value for a + column is used to group the column values into different groups. + + The bin range list is used to group values for a column into + different groups; It must contain values in ascending order. + Examples: + + 10,20,30 + 0.1,0.2,0.3,0.4,0.5 + + 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. + + -h, --help + Print this help message. + + --klargest *number* + Kth largest value to find by *KLargest* function. Default value: + *2*. Valid values: positive integers. + + --ksmallest *number* + Kth smallest value to find by *KSmallest* function. Default values: + *2*. Valid values: positive integers. + + -m, --mode *DescriptiveStatisticsBasic | DescriptiveStatisticsAll | All + | "function1, [function2,...]"* + 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: *DescriptiveStatisticsBasic + | DescriptiveStatisticsAll | "function1,[function2]..."*. Default + value: *DescriptiveStatisticsBasic* + + *DescriptiveStatisticsBasic* includes these functions: *Count, + Maximum, Minimum, Mean, Median, Sum, StandardDeviation, + StandardError, Variance*. + + *DescriptiveStatisticsAll*, in addition to + *DescriptiveStatisticsBasic* functions, includes: *GeometricMean, + Frequency, HarmonicMean, KLargest, KSmallest, Kurtosis, Mode, + RSquare, Skewness, TrimMean*. + + *All* uses complete list of supported functions: *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*. 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: + + Average: See Mean + + AverageDeviation: SUM( ABS(x[i] - Xmean) ) / n + + Correlation: See Pearson Correlation + + Covariance: SUM( (x[i] - Xmean)(y[i] - Ymean) ) / n + + GeometricMean: NthROOT( PRODUCT(x[i]) ) + + HarmonicMean: 1 / ( SUM(1/x[i]) / n ) + + Mean: SUM( x[i] ) / n + + Median: Xsorted[(n - 1)/2 + 1] for even values of n; (Xsorted[n/2] + + Xsorted[n/2 + 1])/2 for odd values of n. + + Kurtosis: [ {n(n + 1)/(n - 1)(n - 2)(n - 3)} SUM{ ((x[i] - + Xmean)/STDDEV)^4 } ] - {3((n - 1)^2)}/{(n - 2)(n-3)} + + PearsonCorrelation: SUM( (x[i] - Xmean)(y[i] - Ymean) ) / SQRT( SUM( + (x[i] - Xmean)^2 ) (SUM( (y[i] - Ymean)^2 )) ) + + RSquare: PearsonCorrelation^2 + + Skewness: {n/(n - 1)(n - 2)} SUM{ ((x[i] - Xmean)/STDDEV)^3 } + + StandardDeviation: SQRT ( SUM( (x[i] - Mean)^2 ) / (n - 1) ) + + StandardDeviationN: SQRT ( SUM( (x[i] - Mean)^2 ) / n ) + + StandardError: StandardDeviation / SQRT( n ) + + StandardScore: (x[i] - Mean) / (n - 1) + + StandardScoreN: (x[i] - Mean) / n + + Variance: SUM( (x[i] - Xmean)^2 / (n - 1) ) + + VarianceN: SUM( (x[i] - Xmean)^2 / n ) + + -o, --overwrite + Overwrite existing files. + + --outdelim *comma | tab | semicolon* + Output text file delimiter. Possible values: *comma, tab, or + semicolon* Default value: *comma*. + + -p, --precision *number* + Precision of calculated values in the output file. Default: up to + *2* decimal places. Valid values: positive integers. + + -q, --quote *yes | no* + Put quotes around column values in output text file. Possible + values: *yes or no*. Default value: *yes*. + + -r, --root *rootname* + 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. + + --trimfraction *number* + Fraction of data to exclude from the top and bottom of the data set + during *TrimMean* calculation. Default value: *0.1* Valid values: > + 0 and < 1. + + -w --workingdir *text* + Location of working directory. Default: current directory. + +EXAMPLES + To calculate basic statistics for data in all common data fields and + generate a NewSample1DescriptiveStatisticsBasic.csv file, type: + + % AnalyzeSDFilesData.pl -o -r NewSample1 Sample1.sdf + + To calculate basic statistics for MolWeight data field and generate a + NewSample1DescriptiveStatisticsBasic.csv file, type: + + % AnalyzeSDFilesData.pl --datafields MolWeight -o -r NewSample1 + Sample1.sdf + + 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: + + % AnalyzeSDFilesData.pl -m DescriptiveStatisticsAll --datafields + MolWeight -o --datafieldpairs AllPairs -r NewSample1 Sample1.sdf + + To compute frequency distribution of MolWeight data field into five bins + and generate NewSample1MolWeightFrequencyAnalysis.csv, type: + + % AnalyzeSDFilesData.pl -m Frequency --frequencybins 5 --datafields + MolWeight -o -r NewSample1 Sample1.sdf + + To compute frequency distribution of data in MolWeight data field into + specified bin range values, and generate + NewSample1MolWeightFrequencyAnalysis.csv, type: + + % AnalyzeSDFilesData.pl -m Frequency --frequencybins "100,200,400" + --datafields MolWeight -o -r NewSample1 Sample1.sdf + + To calculate all available statistics for data in all data fields and + pairs, type: + + % AnalyzeSDFilesData.pl -m All --datafields All --datafieldpairs + AllPairs -o -r NewSample1 Sample1.sdf + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, + MergeTextFilesWithSD.pl + +COPYRIGHT + Copyright (C) 2015 Manish Sud. All rights reserved. + + This file is part of MayaChemTools. + + 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. +