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<p>Automatic synchronization with BioUML</p> <p><b>New page</b></p><div>;Analysis title<br /> :[[File:Statistics-LRPath-icon.png]] LRPath<br /> ;Provider<br /> :[[geneXplain GmbH]]<br /> ;Class<br /> :{{Class|com.genexplain.stat.LRPath}}<br /> ;Plugin<br /> :[[Com.genexplain.stat (plugin)|com.genexplain.stat (geneXplain Stat)]]<br /> <br /> === LRPath enrichment analysis ===<br /> <br /> LRPath is a Gene Set Enrichment Analysis (GSEA) method that uses logistic regression models to discover categories that are significantly correlated with a predictor &lt;nowiki&gt;[&lt;/nowiki&gt;1&lt;nowiki&gt;]&lt;/nowiki&gt;. The predictor can be the (-log) P-value of differential expression or another quantity. By default, predictors are treated as P-values, which means they are -log-transformed and set to a maximum of [https://docs.oracle.com/javase/8/docs/api/java/lang/Double.html#MAX_EXPONENT java.lang.Double.MAX_EXPONENT] if 0.<br /> <br /> The analysis includes selection of significant genes. This requires that a quantity is specified and a cut-off by which significance is determined. The values used for this purpose can be provided in another column than the predictor.<br /> <br /> ==== Parameters ====<br /> <br /> * '''Input table''' - Path to table with input data<br /> * '''Species''' - Species of genes in the input table<br /> * '''Classification''' - Classification you want to use. List of classifications may differ depending on software version and your subscription<br /> * '''Predictor column''' - Column with the LR predictor variable<br /> * '''Treat predictors as P-values''' - Indicates whether predictors shall be treated as P-values (-log-transformed and set to a maximum if 0)<br /> * '''Significance column''' - Column with significance values<br /> * '''Significance cutoff''' - Cutoff on significance values to select genes<br /> * '''Significant is lower''' - If true, significant genes must have lower values than the cutoff<br /> * '''Calculations only for classified genes''' - Do calculations only for classified genes, e.g. when the input gene set is much bigger than the annotation database<br /> * '''Result table''' - Path for the result table<br /> <br /> ==== References ====<br /> <br /> # Sartor MA, Leikauf GD, Medvedovic M. LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics. 2009;25(2):211-217.<br /> <br /> [[Category:Analyses]]<br /> [[Category:Statistics (analyses group)]]<br /> [[Category:GeneXplain analyses]]<br /> [[Category:Autogenerated pages]]</div>

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