neuroimaGene {neuroimaGene}R Documentation

Main neuroimaGene query

Description

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.

Usage

neuroimaGene(
  gene_list,
  modality = "T1",
  atlas = "Desikan",
  mtc = "BH",
  nidps = NA,
  filename = NA,
  verbose = FALSE,
  vignette = FALSE
)

Arguments

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

Value

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.

Examples

gene_list <- c('TRIM35', 'PROSER3', 'EXOSC6', 'PICK1', 'UPK1A', 'ESPNL', 'ZIC4')
ng <- neuroimaGene(gene_list, atlas = NA, mtc = 'BH', vignette = TRUE)


[Package neuroimaGene version 0.1.1 Index]