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# 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

# SEE ALSO

FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, MergeTextFilesWithSD.pl

# COPYRIGHT

Copyright (C) 2018 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.

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