CreateBrain: Overlap spatial enrichment information and anatomical...

Description Usage Arguments Value Examples

View source: R/CreateBrain.R

Description

CreateBrain convert spatial enrichment into anatomical coordinates.

Usage

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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

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#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)

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