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

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
#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)

brainImageR documentation built on May 6, 2019, 3:54 a.m.