draw_network: Draw network of enriched functional annotation pairs

In ezer/PAFway: Pairwise Association of Functional Annotations

Description

Draw network of enriched functional annotation pairs

Usage

draw_network(graph, pval = 0.05, adjMethod = NULL, seed = 123)

Arguments

graph	The output of either the pafway or pafway_edge_weight functions
pval	The threshold of p-value at which to draw an arrow
adjMethod	The method for correcting for multiple hypotheses. This can be any method that is acceptable to the p.adjust function in the stats package: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr" or "none". If this is NULL, then no adjustment will be made.
seed	The random seed that will be used.

Value

A matrix that has the same number of rows and columns as length(GOtypes). This will contain p-values.

Examples

a=matrix(c(0.1, 0.003, 0.005, 0.004, 0.5, 0.7, 0.001, 0.002, 0.003), nrow=3)
colnames(a)=c('A', 'B', 'C')
rownames(a)=c('A', 'B', 'C')
draw_network(a)

ezer/PAFway documentation built on Dec. 11, 2019, 12:10 a.m.