neuroimaGene {neuroimaGene}

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.

atlas

Neuroimaging parcellation atlas for NIDP query. Defaults to Desikan structural atlas.

mtc

Statistical multiple testing correction for NIDP query. Defaults to BH for the Benjamini Hochberg False Discovery Rate.

nidps

optional user defined vector of target NIDPs to query. These can be obtained from the listNIDPnames() function.

filename

optional user defined filename for writing neuroimaGene output to a file.

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)