ont.children: Find Ontology Structure Descendants

In DJFernandes/ABIgeneRMINC: Read, Write, and Analyzing Allen Gene Expression Raw Data

Find Ontology Structure Descendants

Description

Given a stucture label in the Allen Brain Atlas, this function will find all its descendants structures in the the grid annotations

Usage

ont.children(parents)

Arguments

parents

Label number of Parent Structure. This parameter is vectorized, so you can specify multiply parents. The return will be a list of same length as the number of parents.

Value

The label number of all descendant structures. These structures can be found in the 200 um grid labels for gene expression analysis

Examples

# In this example, we will find the gene expression of Pdyn in the Hippocampal formation.
# First we download the gene expression file from the Allen Brain Institute
# In this example, I downloaded Pdyn expression energy (http://api.brain-map.org/grid_data/download/71717084)
# Then Unzipped it, and renamed the energy.raw file to Pdyn_energy_experiment71717084.raw 
# I included it in this library as an example

# Also, download Grid Labels from the Allen Brain Institute
# In this example, I downloaded Grid Labels from (http://download.alleninstitute.org/informatics-archive/current-release/mouse_annotation/P56_Mouse_gridAnnotation.zip), then unzipped it.
# I included it in this library as an example though it is a good idea to download it yourself to keep it updated

# Read Gene expression file
genefilename=system.file('extdata/Pdyn_energy_experiment71717084.raw',package="ABIgeneRMINC")
gene.expression=read.raw.gene(genefilename)

# Read Labels 
labelfilename=system.file('extdata/gridAnnotation.raw',package="ABIgeneRMINC")
labels.grid=read.raw.gene(labelfilename,labels=TRUE)

# The hippocampal formation has many Ontology Structure Descendants. We need to find them.
# Find hippocampal formation structure number
data(AllStructureLabels)
parent.label=subset(AllStructureLabels,name=='Hippocampal formation')$id   #the sturcture number is 1089

# Find Descendant labels
child.labels=ont.children(parent.label)[[1]]

# Unionize over all the children
unionize(gene.expression,child.labels,labels.grid)

DJFernandes/ABIgeneRMINC documentation built on March 21, 2022, 12:05 p.m.