consensus_trait_cor: Correlate set-specific modules and consensus modules to...

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

Correlate set-specific modules and consensus modules to sample information

Description

Correlate set-specific modules and consensus modules to sample information

Usage

consensus_trait_cor(consensus, cor_method = "pearson", metadata_cols = NULL)

Arguments

consensus	Consensus network returned by consensus_modules.
cor_method	Correlation method to be used. One of 'spearman' or 'pearson'. Default: 'pearson'.
metadata_cols	A vector (either numeric or character) indicating which columns should be extracted from column metadata if exp is a 'SummarizedExperiment' object. The vector can contain column indices (numeric) or column names (character). By default, all columns are used.

Value

Data frame of consensus module-trait correlations and p-values, with the following variables:

trait

Factor, trait name. Each trait corresponds to a variable of the sample metadata (if numeric) or levels of a variable (if categorical).

ME

Factor, module eigengene.

cor

Numeric, correlation.

pvalue

Numeric, correlation P-values.

group

Character, name of the metadata variable.

Examples

set.seed(12)
data(zma.se)
filt.zma <- filter_by_variance(zma.se, n=500)
zma.set1 <- filt.zma[, sample(colnames(filt.zma), size=20, replace=FALSE)]
zma.set2 <- filt.zma[, sample(colnames(filt.zma), size=20, replace=FALSE)]
list.sets <- list(zma.set1, zma.set2)
# SFT power previously identified with consensus_SFT_fit()
consensus <- consensus_modules(list.sets, power = c(11, 13),
                               cor_method = "pearson")
consensus_trait <- consensus_trait_cor(consensus, cor_method = "pearson")

almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.