JBA_corDistribution: Setting the ct threshold for JBA

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

Description

This function compares the distribution of correlations between st adjacent variables in a spectral region dominated by noise and a spectral region dominated by metabolic signals. This function can be used to set the ct threshold for JBA binning.

Usage

JBA_corDistribution(NMR_data, st = 4, cm = "pearson", metabo_range = c(3.50, 3.96),
                    noise_range = c(9.72, 9.99), color_scale = c("lightcoral", "honeydew3"))

Arguments

NMR_data	numeric matrix containing the NMR data (i.e. NMR peak intensities). The columns of the matrix must correspond to the metabolic variables (chemical shifts) and the rows to the samples. Column and row names must contain the metabolite IDs (i.e chemical shifts) and the sample IDs, respectively.
st	numeric value indicating the minimum bin size.
cm	character vector specifying the correlation method ("pearson" or "spearman").
metabo_range	numeric vector indicating the limits of a spectral region dominated by metabolic signals.
noise_range	numeric vector indicating the limits of a spectral region dominated by noise.
color_scale	character vector indicating color of the metabolic curve (first value), and the noise curve (second value).

Value

A plot comparing the distribution of average correlations between st adjacent variables in a spectral region dominated by metabolic signals (metabo_range) and in a spectral region dominated by electronic noise (noise_range). The suggested ct value corresponds to the correlation coefficient where the cumulative proportion of noise clusters is 1.

Examples

## Not available.

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