make.cor.matrix: correlation matrix

In MRCIEU/metaboprep: Metabolomics data preparation and processing pipeline

correlation matrix

Description

This function estimates a correlation matrix returning wither the correlation estimates or their p-values

Usage

make.cor.matrix(wdata, cor_method = "kendall", minN = 50, var2return = "cor")

Arguments

wdata	the metabolite data matrix. samples in row, metabolites in columns
cor_method	defaulted to "kendall" this is the correlation method to use in the function cor.test()
minN	sefaulted to 50, this is the minimum number of observations that must be available in pairs to perform analysis
var2return	sefaulted to "cor", other option is "pvalue" is a the flag indicating which estimate to return from the function.

Value

a matrix of correlation estimates or p-values

Examples

cmat = matrix(1, 4, 4 )
cmat[1,] = c(1, 0.8, 0.6, 0.2)
cmat[2,] = c(0.8, 1, 0.7, 0.5)
cmat[3,] = c(0.6, 0.7, 1, 0.6)
cmat[4,] = c(0.2, 0.5, 0.6,1)
## simulate some correlated data (multivariable random normal)
set.seed(1110)
ex_data = MASS::mvrnorm(n = 250, mu = c(5, 45, 25, 15), Sigma = cmat )
## return correlation estimates
cor_mat = make.cor.matrix(ex_data, var2return = "cor")
## return p-values
cor_mat = make.cor.matrix(ex_data, var2return = "pvalue")

MRCIEU/metaboprep documentation built on Jan. 28, 2023, 7:29 p.m.