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LANDD (version 1.1.0)

Liquid Association for Network Dynamics Detection

Description

Using Liquid Association for Network Dynamics Detection.

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Version

Install

install.packages('LANDD')

Monthly Downloads

4

Version

1.1.0

License

GPL (>= 2)

Maintainer

Shangzhao Qiu

Last Published

October 1st, 2016

Functions in LANDD (1.1.0)

Find the liquid association scouting genes.

Create a table to record Gene Ontology Biological Process mapping results. Every gene W's community takes a row.

normalizeInputMatrix

Normalize the input Matrix

Find weights based on kernel density on the graph. There are three common ways to invoke graph.kd:

graph.kd(relate_matrix, graph, smoothing.normalize=c('one'))
graph.kd(relate_matrix, graph, smoothing.normalize=c('squareM'))
graph.kd(relate_matrix, graph, smoothing.normalize=c('none'))

The first method is used when the total weight of all genes z is set to 'one'. In this way, those genes surrounded by more genes z will not take advantages over those surrounded by fewer genes. In contrast, the second method takes the number of genes around into consideration, the result of the first method will multiply the square of the number of genes around. The third method does not normalize the data. Thus genes with more neighbors are more likely to receive higher weights.

Create a table to record the distance between gene x and gene w.

Visualize: Generate a graph which vividly displays the gene X, Y and W.

visualize.community

visualize ego gene X, its k step neighbours, and the W gene communities: Generate a graph with different community in different colors. visualize.community()is used to create a graph to display the layout of genes X, X's k-step neighborhood, W and their corresponding community.