PValue.onetail: Calculate p-value from bootstrapped sample

In saralinker/brainImageR: A Framework for visualizing gene set enrichment throughout neurodevelopment

Description

The distribution of microdissected tissues supporting each larger brain region is not equal across all regions. We therefore provide an option to bootstrap gene set enrichment. This function calculates the signficance of that enrichment.

PValue.onetail Calculates the p-value from a bootstrapped sample

Usage

PValue.onetail(regions, tissueExp1, random.matrix)

Arguments

regions	character regions to search
tissueExp1	numeric vector presence of genes in query
random.matrix	numeric presence of genes at random

Value

p-value of the significance of tissueExp1 given the random.matrix

Examples

##Internal to brainImageR, called within testEnrich
#brainImageR:::loadworkspace()
##First put together a gene list, or load in the default vth dataset
data(vth)
##Calculate the spatial enrichment.
#composite <- SpatialEnrichment(vth, reps = 20, refset = "developing")
#tissueExp1 <- composite@tissueExp1
#random.matrix <- [e-mail]
#boot <- PValue.onetail(regions = names(tissueExp1),
#tissueExp1,
#random.matrix)

saralinker/brainImageR documentation built on May 29, 2019, 1:51 p.m.