associate: Cross Correlation Wrapper

In microbiome/microbiome: Microbiome Analytics

Cross Correlation Wrapper

Description

Cross-correlate columns of the input matrices.

Usage

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
)

Arguments

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	minimum 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.

Details

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.

Value

List with cor, pval, pval.adjusted

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation('microbiome')

Examples

data(peerj32)
d1 <- peerj32$microbes[1:20, 1:10]
d2 <- peerj32$lipids[1:20,1:10]
cc <- associate(d1, d2, method='pearson')

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.