Code of structural entropy minimisation for TAD identification of Hic matrix
Switch branches/tags
Nothing to show
Clone or download
Latest commit 839bf46 Sep 7, 2018
Failed to load latest commit information. Update Sep 7, 2018
deDoc.rar Add files via upload Sep 7, 2018


The java code of algorithm of structure entroy minimisation example java -jar structureEntropy.jar xxx/xxx/xxx/hicGraph

We treat Hic matrix as the adjacent matrix of the hicGraph which is the input of this algorithm. The format is 3 1 2 1.0 1 3 2.0 2 3 3.0 The first line is the number of bins in the graph The second line is the edge: first_bin second_bin reads .splitted by space. The node_id start from 1. Resultfile (hicGraph.deDoc(E) or hicGraph.deDoc(M)) is the result of communities found by algorithm deDoc(E) or deDoc(M). Each line is a tad. And it will print the 2D-nSE of the hicGraph.

To compute 1D-nSE, use command java -jar onednSE.jar xxx/xxx/xxx/hicGraph The result is the 1D-nSE of this hicGraph.

To get the java source code, you just need to decompress structureEntropy.jar and onednSE.jar using software such as WinRAR.

P.S. The input Hi-C matrix should be symmetric matrix