correlation {MetNet} | R Documentation |
'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.
correlation(x, type = "pearson", p.adjust = "none")
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". |
p.adjust |
'character', method of p-value adjustment passed to 'p.adjust' |
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).
matrix, matrix with edges inferred from correlation algorithm 'corAndPvalue', 'pcor' or 'spcor' (depending on the chosen 'method')
Thomas Naake, thomasnaake@googlemail.com
data("x_test", package = "MetNet") x <- x_test[1:10, 3:ncol(x_test)] x <- as.matrix(x) correlation(x, type = "pearson")