CreateBrain {brainImageR}R Documentation

Overlap spatial enrichment information and anatomical organization

Description

CreateBrain convert spatial enrichment into anatomical coordinates.

Usage

CreateBrain(composite, boot, slice, pcut = 0.05)

Arguments

composite

Comp object returned from SpatialEnrichment

boot

result from testEnrich including significance estimates

slice

integer brain section

pcut

numeric padj filter.

Value

Comp object

Examples

#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 <- composite@random.matrix
##Calculate the significance estimates
#boot <- testEnrich(composite)
##Color the brain section of interest with enrichment
#composite <- CreateBrain(composite, boot, slice = 6, pcut = 0.05)
##Plot the brain
#PlotBrain(composite, Breaks = 12)

[Package brainImageR version 1.0.0 Index]