CreateBrain: Overlap spatial enrichment information and anatomical...
In saralinker/brainImageR: A Framework for visualizing gene set enrichment throughout neurodevelopment
Description
Usage
Arguments
Value
Examples
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
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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.
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Description Usage Arguments Value Examples
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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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