Retrieve the reference correlation matrix for clock gene co-expression.

Source: R/deltaccd.R

The reference matrix is based on a fixed-effects meta-analysis of eight circadian transcriptome datasets from mice, as described in Shilts et al. 2018.

getRefCor(species = "human", useEntrezGeneId = TRUE)

Arguments

species

Currently either 'human' or 'mouse'. Only affects the row and column names of the correlation matrix, not the actual values.
useEntrezGeneId

If FALSE, row and column names of correlation matrix will correspond to gene symbols (e.g., PER2).

Value

A matrix of Spearman correlation values.

See also

GSE19188, plotRefHeatmap(), calcCCD(), calcDeltaCCD()

Examples

if (FALSE) {
library('deltaccd')
library('doParallel')
library('doRNG')

registerDoParallel(cores = 2)
set.seed(35813)

refCor = getRefCor()
ccdResult = calcCCD(refCor, GSE19188$emat, GSE19188$groupVec, dopar = TRUE)
deltaCcdResult = calcDeltaCCD(refCor, GSE19188$emat, GSE19188$groupVec,
                              'non-tumor', dopar = TRUE)

pRef = plotRefHeatmap(refCor)
pTest = plotHeatmap(rownames(refCor), GSE19188$emat, GSE19188$groupVec)
}