edgefinder
Note Staring from version 0.1.9, the repository has been relocated to https://github.com/haimbar/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.
See vignettes/edgefinder.md for details.