pBoot: Bootstrap path p-value

In aarkatkar/gelClust: Clustering and pathway analysis using exponential distributions

Bootstrap path p-value

Description

Obtain a p-value for a minPath by comparison to a bootstrap distribution obtained by distBoot.

Usage

pBoot(d, z)

Arguments

d	Output of the distBoot function
z	The minimal path length to be tested

Value

A bootstrap p-value

Author(s)

Anooj Arkatkar

See Also

minPath, distBoot

Examples

# Load data
data(foldChange)
data(traitData)

# Obtain clusters
c.gm <- gelMatrix(foldChange)
clust <- gammaCluster(c.gm, 7)

# Set up the path data
path.gm <- gelMatrix(foldChange, phen=traitData, squared=TRUE, output="orig")
nodeNames <- c(rownames(traitData), rownames(foldChange))

# Find the minimal path
mp <- minPath("TCDD", "Fat", path.gm, clust$labels, nodeNames=nodeNames)

# Obtain the p-value
bdist <- distBoot(foldChange)
p <- pBoot(bdist, sum(mp$pvals))

aarkatkar/gelClust documentation built on May 6, 2022, 12:24 a.m.