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README.md

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+# edgefinder
+The edgefinder package is used to find edges in gene networks using co-expression
+data. The input to the program is a normalized expression matrix, with genes (nodes)
+in the rows, and samples in the columns.
+The program calculates the pair-wise correlations, performs Fisher's Z 
+transformation, and fits the L2N model to the transformed data. L2N is a mixture
+model with three components: the uncorrelated pairs belong to the null component
+which is assumed to be normally distributed, and the correlated pairs belong to one
+of the two non-null components which are assumed to follow lognormal distributions.
+
+Typical datasets consist of hundreds, or thousands of genes, and hence a very
+large number of pairs. Therefore, edgefinder randomly selects a subset of the pairs (the
+default number of pairs is 20,000), fits the L2N model to the subset, and calculates
+the component probabilities for *all* possible pairs.
+Using the posterior probabilities, edgefinder determines which pairs are
+highly correlated while controlling the false discovery rate.
+Note that edgefinder makes no assumptions about the structure of the network.
+
+The edgefinder package depends on the 'Matrix' package, to allow for efficient
+storage and computation of large co-occurrence matrices. For simulating datasets
+we used the 'huge' and 'MASS' packages, but they are not required when
+using edgefinder.