visualiseSNP: Visualise by-voxel statistics for a chosen SNP, e.g that...

In JakubBartoszewicz/RImaGen: Fast Voxelwise Genome-Wide Association Studies in R

Description

Visualise by-voxel statistics for a chosen SNP, e.g that SNP's p-value per voxel.

Usage

visualiseSNP(snp.name, results, mask, ref.img, pv.range = NULL,
  log.cutoff = 0, plot = TRUE, title = snp.name, titleSize = 2,
  beforeTitle = "-log10 p-values by\n", afterTitle = "", outPath = NULL,
  matPath = NULL, coordsOnly = FALSE)

Arguments

snp.name	Chosen SNP name.
results	A named list of results for each SNP.
mask	Image mask (a nifti object or an array).
ref.img	Reference image.
pv.range	P-value range for scale.
log.cutoff	Negative log p-value cutoff value.
plot	logical. Set to TRUE for automated plotting of the results.
title	Plot title.
titleSize	Title font size.
beforeTitle	Text to print before the title.
afterTitle	Text to print after the title.
outPath	Output path. If NULL (default) no plot files will be saved.
matPath	Path to convolution matrix for coregistration of results to the reference image. Set to NULL if in the same space.
coordsOnly	logical. Set to TRUE to return coordinates of the best voxel only.

Value

A list containing the results visualisation image and a vector of coordinates for the max. value voxel.

JakubBartoszewicz/RImaGen documentation built on May 8, 2017, 11:21 p.m.