STOCSY_NMR: Statistical Total Correlation Spectroscopy - Academic use...

In MWASTools: MWASTools: an integrated pipeline to perform metabolome-wide association studies

Description

This function calculates STOCSY between an NMR signal of interest and all the NMR variables, representing a useful tool for NMR molecular identification and assignment. The results are represented in a pseudo-NMR spectrum displaying the covariance (height) and the Pearson/Spearman correlation coefficient (color) of all spectral variables with the variable of interest (driver signal).

Usage

STOCSY_NMR (metabo_SE, ppm_query, cor_method = "pearson", alpha_th = 0.05,
            xlab = "ppm", ylab = "covariance", size_lab = 12, size_axis = 12,
            xlim = NULL, ylim = NULL, xbreaks = waiver(), xnames = waiver(),
            ynames = waiver(), ybreaks = waiver())

Arguments

metabo_SE	SummarizedExperiment object. See "MWAS_SummarizedExperiment()".
ppm_query	numeric value (at least 2 decimals) corresponding to the driver ppm.
cor_method	character vector specifying the correlation method("pearson" or "spearman").
alpha_th	numeric value indicating the significance threshold. NMR variables with BH-adjusted p-value equal or above this threshold will be neglected.
xlab	character vector specifying a title for the x-axis.
ylab	character vector specifying a title for the y-axis.
size_lab	numeric value indicating the font size of x- and y- axis titles.
size_axis	numeric value indicating the font size of x- and y- axis labels.
xlim	numeric vector containing the minimum and maximum values of the x-axis. Notice that ppm is displayed in reverse scale (e.g. xlim = c(2, 1)).
ylim	numeric vector containing the minimum and maximum values of the y-axis.
xbreaks	numeric vector indicating the positions of the breaks of the x-axis.
xnames	character vector (same length as xbreaks) containing the labels of each break of the x-axis.
ybreaks	numeric vector indicating the positions of the breaks of the y-axis.
ynames	character vector (same length as ybreaks) containing the labels of each break of the y-axis.

Value

A plot displaying the Pearson correlation coefficient (color) and covariance (height) between all spectral variables and the driver signal.

References

Cloarec O, et al.(2005). Statistical total correlation spectroscopy: An exploratory approach for latent biomarker identification from metabolic 1H NMR data sets. Analytical Chemistry, 77, 1282???1289.

Nicholson JK, et al. (2005). Method for the identification of molecules and biomarkers using chemical, biochemical and biological data. US 20070043518 A1

Examples

## Load data
data(metabo_SE)

## STOCSY using 1.04 as driver signal
STOCSY_NMR (metabo_SE, ppm_query = 1.04)
STOCSY_NMR (metabo_SE, ppm_query = 1.04, alpha_th = 0, xlim = c(1.06, 1))

MWASTools documentation built on Nov. 8, 2020, 5:07 p.m.