unionize: Sum Grid Values over Labels

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

Sum Grid Values over Labels

Description

Using this function you can add the gene expression voxels within a particular label. This allows you to find gene expression of any gene in a particular structure.

Usage

unionize(grid.data, labels.to.sum, labels.grid, neg.rm = TRUE)

Arguments

grid.data	1D vector of voxels to sum over (fro example gene expression data)
labels.to.sum	The struction labels you want to unionize over. This is parameter is vectorized so you can sum over multiple labels and get statistical data for each label seperately
labels.grid	1D vector of labels (must be registered to grid.data)
neg.rm	Remove negative data for unionization (negative gene expression means there is no data there)

Value

data frame with labels as rows; and columns with sum, mean, and Standard Deviation of unionized grid.data

Examples

# In this example, we will find the gene expression of Pdyn in the Paraventricular Nucleus of the Thalamus.
# 
# 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)

# Find Label Number Corresponding to Paraventricular Nucleus of the Thalamus
data(GridStructureLabels)
label.num=subset(GridStructureLabels,name=='Paraventricular nucleus of the thalamus')$id
# Paraventricular nucleus of the thalamus corresponds to label 149 in labels.grid

# Unionize to find gene expression in the Paraventricular nucleus of the thalamus
unionize(gene.expression,label.num,labels.grid)

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