From 4f607fb5e2a3c476ef66fb6f41b42be0e0f6c713 Mon Sep 17 00:00:00 2001 From: Haim Bar Date: Wed, 29 Jul 2020 22:47:16 -0400 Subject: [PATCH] Create README.md --- README.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..9bbd5b9 --- /dev/null +++ b/README.md @@ -0,0 +1,22 @@ +# 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.