STOCSY_NMR {MWASTools} | R Documentation

## Statistical Total Correlation Spectroscopy - Academic use only

### 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))

[Package MWASTools version 1.14.0 Index]