correlation: Create an adjacency matrix based on correlation

In MetNet: Inferring metabolic networks from untargeted high-resolution mass spectrometry data

Description

'correlation' infers an adjacency matrix using correlation using the 'cor' function (from the 'stats' package), 'pcor' (from 'ppcor') or 'spcor' (from 'ppcor'). 'correlation' extracts the reported pair-wise correlation coefficients from the function 'corAndPvalue', 'pcor' or 'spcor' and will return the weighted adjacency matrix of the absolute correlation values.

Usage

correlation(x, type = "pearson", use = "pairwise.complete.obs")

Arguments

x	matrix, where columns are the samples and the rows are features (metabolites), cell entries are intensity values
type	'character', either "pearson", "spearman", "pearson_partial", "spearman_partial", "pearson_semipartial" or "spearman_semipartial".
use	'character' string giving a method for computing covariance in the presence of missing values, Only for 'type = "pearson"' or 'type = "spearman"'. For further information see '?stats::cor'

Details

If '"pearson"' or '"spearman"' is used as a 'method', the function 'corAndPvalue' from 'stats' will be employed.

If '"pearson_partial"' or '"spearman_partial"?' is used as a 'method' the function 'pcor' from 'spcor' will be employed.

If '"pearson_semipartial"' or '"spearman_semipartial"' is used as a 'method' the function 'spcor' from 'spcor' will be employed.

'type' will be passed to argument 'method' in 'cor' (in the case of '"pearson"' or '"spearman"') or to 'method' in 'pcor' ('"pearson"' and '"spearman"' for '"pearson_partial"' and '"spearman_partial"', respectively) or to 'method' in 'spcor' ('"pearson"' or '"spearman"' for '"pearson_semipartial"' and '"spearman_semipartial"', respectively).

Value

matrix, matrix with edges inferred from correlation algorithm 'corAndPvalue', 'pcor' or 'spcor' (depending on the chosen 'method')

Author(s)

Thomas Naake, [e-mail]

Examples

data("x_test", package = "MetNet")
x <- x_test[1:10, 3:ncol(x_test)]
x <- as.matrix(x)
correlation(x, type = "pearson")

MetNet documentation built on Nov. 8, 2020, 7:34 p.m.