Title: | Transcriptomic Atlas of Neuroimaging Derived Phenotypes |
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Description: | Contains functions to query and visualize the Neuroimaging features associated with genetically regulated gene expression (GReX). The primary utility, neuroimaGene(), relies on a list of user-defined genes and returns a table of neuroimaging features (NIDPs) associated with each gene. This resource is designed to assist in the interpretation of genome-wide and transcriptome-wide association studies that evaluate brain related traits. Bledsoe (2024) <doi:10.1016/j.ajhg.2024.06.002>. In addition there are several visualization functions that generate summary plots and 2-dimensional visualizations of regional brain measures. Mowinckel (2020). |
Authors: | Xavier Bledsoe [aut, cre] , Eric Gamazon [aut] |
Maintainer: | Xavier Bledsoe <[email protected]> |
License: | GPL (>= 3) |
Version: | 0.1.2 |
Built: | 2024-12-09 09:40:33 UTC |
Source: | CRAN |
annotation data for all NIDPs taken from the UKbiobank
A data.table with 10 columns and 3935 rows:
character: UKB-derived neuroimaging derived phenotype (NIDP)
character: MRI neuroimaging modality
character: neuroimaging cortical atlas
character: right or left hemisphere or midline/whole brain
character: primary cortical region
character: secondary cortical region
character: named region of the brain
character: morphology measurement
character: fMRI node 1
character: fMRI node 2
character: user-friendly name for each NIDP
This script has no return. This is a documentation file for the annotation dataset for all neuroimaging derived phenotypes.
Bledsoe, X. (2024) A transcriptomic atlas of the human brain reveals genetically determined aspects of neuropsychiatric health
Check if the NeuroimaGene database exists in the proper location prior to running the query and prompt user to download if not.
check_db(timeout = 900)
check_db(timeout = 900)
timeout |
time to spend downloading the NeuroimaGene database in seconds (default = 900) |
no return value, called to give information on status of neuroimaGene database and prompt user the user to download if resource file is missing.
check_db(timeout = 600)
check_db(timeout = 600)
Freesurfer names for select cortical and subcortical NIDPs
data(fs_anno)
data(fs_anno)
A data.table with 7 columns and 890 rows:
character: UKB-derived neuroimaging derived phenotype
character: neuroimaging cortical atlas
character: right or left hemisphere or midline/whole brain
character: secondary cortical region
character: freesurfer name
character: label name for the region
character: freesurfer name for neuroimaging cortical atlas
This script has no return. This is a documentation file for the annotation dataset for all neuroimaging derived phenotypes in the fsbrain package.
Bledsoe, X. (2024) A transcriptomic atlas of the human brain reveals genetically determined aspects of neuropsychiatric health
Supplies a list of all NIDPs by name for any given modality or atlas
listNIDPs(modality = NA, atlas = NA, filename = NA, verbose = FALSE)
listNIDPs(modality = NA, atlas = NA, filename = NA, verbose = FALSE)
modality |
Neuroimaging modality. Defaults to NA; see README for additional options |
atlas |
Neuroimaging parcellation atlas for NIDP query. Defaults to NA; see README for additional options |
filename |
optional filename for writing data to a table |
verbose |
print runtime messages to R console. Default to FALSE |
a list of NIDP names satisfying the required criteria
dk_names <- listNIDPs(modality = 'T1', atlas = 'Desikan')
dk_names <- listNIDPs(modality = 'T1', atlas = 'Desikan')
Generates a 2D visualization plot of the neuroimaGene object. Neuroimaging regions are defined by the atlas parameter and colored according to the magnitude and direction of the aggregate effect from each gene in the NeuroimaGene object. Colors can be defined by the user.
neuro_vis( ng_obj, atlas = "Desikan", lowcol = "red2", midcol = "white", highcol = "royalblue2", title = NA )
neuro_vis( ng_obj, atlas = "Desikan", lowcol = "red2", midcol = "white", highcol = "royalblue2", title = NA )
ng_obj |
NeuroimaGene object produced by neuroimaGene() function |
atlas |
desired atlas for visualization. Desikan (default), Subcortex, DKT, Destrieux. |
lowcol |
color for low end of Zscore spectrum. Default is dark red |
midcol |
color for middle of Zscore spectrum. Default is white |
highcol |
color for top end of Zscore spectrum. Default is blue4 |
title |
optional title tag for the plot |
class: ggplot object depicting 2D visualization of the NIDPs from the neuroimaGene object portrayed on the brain and shaded by mean effect size.
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE) neuro_vis(ng, atlas = 'DKT')
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE) neuro_vis(ng, atlas = 'DKT')
Using a user supplied vector of genes (Ensembl ID's or HUGO names), this function queries the NeuroimaGene resource for all statistically significant GReX-NIDP associations and returns all findings as a data.table.
neuroimaGene( gene_list, modality = "T1", atlas = "Desikan", mtc = "BH", nidps = NA, filename = NA, verbose = FALSE, vignette = FALSE )
neuroimaGene( gene_list, modality = "T1", atlas = "Desikan", mtc = "BH", nidps = NA, filename = NA, verbose = FALSE, vignette = FALSE )
gene_list |
List of genes to work as inputs. There are no defaults. |
modality |
Neuroimaging modality for NIDP query. Defaults to T1 structural NIDPs. Other common options include 'dMRI' for diffusion MRI imaging and 'fMRI' for fucntional MRI image results. |
atlas |
Neuroimaging parcellation atlas for NIDP query. Defaults to Desikan structural atlas. Common T1 atlases include the 'DKT', and 'Destrieux' cortical atlases and 'Subcortex' for freesurfer parcellation of subrotical regions. See package documentation or vignette for full list. |
mtc |
Statistical multiple testing correction for NIDP query. This defaults to 'BH' for the Benjamini Hochberg False Discovery Rate. Other options include 'BF' for the bonferroni family wise error rate and 'nom' for nominal findings at pvalue <= 0.05. |
nidps |
optional user defined vector of target NIDPs to query. Specific NIDP names can be obtained from the listNIDPnames() function. Use of this parameter overrides the multiple testing correction, returning all nominally significant findings. |
filename |
optional user defined path/filename to which the script will write the nueroimaGene output data table. |
verbose |
print runtime messages to R console. Default to FALSE |
vignette |
use for building vignette on installation. Default to FALSE |
a neuroimaGene object: data table with all significant associations between the user provided genes and the UKB NIDPs satisfying the multiple testing correction and atlas/modality/name filters.
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE)
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE)
NeuroimaGene data table containing select associations used in the package vignette.
data(ng_vignette)
data(ng_vignette)
A data.table with 6 columns and 3824 rows:
character: ENSEMBL Gene ID
character: HUGO gene name
character: neuroimaging derived phenotype
character: JTI derived tissue gene expression model
numeric: normalized effect size of GReX on NIDP morphology
character: Benjamini Hochberg corrected pvalue corrected by modality
This script has no return. This is a documentation file for the neuroimaGene data subset required to build the vignette.
Bledsoe, X. (2024) A transcriptomic atlas of the human brain reveals genetically determined aspects of neuropsychiatric health
Generate overview plot of the neuroimagene object according to gene/NIDP pair
plot_gnNIDP( ng_obj, maxNidps = 20, maxGns = 15, title = NA, shortnames = TRUE, verbose = FALSE )
plot_gnNIDP( ng_obj, maxNidps = 20, maxGns = 15, title = NA, shortnames = TRUE, verbose = FALSE )
ng_obj |
NeuroimaGene object |
maxNidps |
maximum number of NIDPs to visualize. default=20 |
maxGns |
maximum number of genes to visualize. default=15 |
title |
optional title tag for the plot |
shortnames |
optional boolean tag for simplified names. Default to TRUE |
verbose |
print runtime messages to R console. Default to FALSE |
a ggplot class heatmap showing tissue models per NIDP/Gene pair
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE) plot_gnNIDP(ng)
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE) plot_gnNIDP(ng)
Generates an overview plot of the neuroimaGene object according to each gene input.
plot_gns(ng_obj, maxGns = 15, title = NA, verbose = FALSE)
plot_gns(ng_obj, maxGns = 15, title = NA, verbose = FALSE)
ng_obj |
NeuroimaGene Object |
maxGns |
maximum number of genes to visualize. default=15 |
title |
optional title tag for the plot |
verbose |
print runtime messages to R console. Default to FALSE |
a ggplot class plot detailing NIDPs per gene, colored by brain measure type
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE) plot_gns(ng)
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE) plot_gns(ng)
Generate overview plot of the neuroimagene object according to nidps
plot_nidps( ng_obj, maxNidps = 30, title = NA, shortnames = TRUE, mag = TRUE, verbose = FALSE )
plot_nidps( ng_obj, maxNidps = 30, title = NA, shortnames = TRUE, mag = TRUE, verbose = FALSE )
ng_obj |
NeuroimaGene Object |
maxNidps |
maximum number of NIDPs to visualize. default=30 |
title |
optional title tag for the plot |
shortnames |
optional boolean tag for simplified names. Default to TRUE |
mag |
boolean to present effect sizes by magnitude rather than as a vector. Default to TRUE |
verbose |
print runtime messages to R console. Default to FALSE |
a ggplot class object detailing mean effect size magnitude per NIDP, colored by brain region
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE) plot_nidps(ng)
gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4') ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE) plot_nidps(ng)