PAFway (version 0.1.3)

draw_network: Draw network of enriched functional annotation pairs

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

# NOT RUN {
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)
# }