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