associate {microbiome} | R Documentation |
Cross-correlate columns of the input matrices.
associate( x, y = NULL, method = "spearman", p.adj.threshold = Inf, cth = NULL, order = FALSE, n.signif = 0, mode = "table", p.adj.method = "fdr", verbose = FALSE, filter.self.correlations = FALSE )
x |
matrix (samples x features if annotation matrix) |
y |
matrix (samples x features if cross-correlated with annotations) |
method |
association method ('pearson', or 'spearman' for continuous) |
p.adj.threshold |
q-value threshold to include features |
cth |
correlation threshold to include features |
order |
order the results |
n.signif |
mininum number of significant correlations for each element |
mode |
Specify output format ('table' or 'matrix') |
p.adj.method |
p-value multiple testing correction method. One of the methods in p.adjust function ('BH' and others; see help(p.adjust)). Default: 'fdr' |
verbose |
verbose |
filter.self.correlations |
Filter out correlations between identical items. |
The p-values in the output table depend on the method. For the spearman and pearson correlation values, the p-values are provided by the default method in the cor.test function.
List with cor, pval, pval.adjusted
Contact: Leo Lahti microbiome-admin@googlegroups.com
See citation('microbiome')
data(peerj32) d1 <- peerj32$microbes[1:20, 1:10] d2 <- peerj32$lipids[1:20,1:10] cc <- associate(d1, d2, method='pearson')