Description Usage Arguments Value See Also Examples
Quantify the similarity of gene co-expression between a reference and a test dataset. Statistical significance is calculated using permutation of the genes.
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refCor |
Correlation matrix to be used as the reference, such as comes
from |
emat |
Matrix of expression values, where each row corresponds to a
gene and each column corresponds to a sample. The rownames and colnames of
|
groupVec |
Optional vector indicating the group to which group each sample belongs. If not provided, the function assumes all samples belong to the same group. |
refEmat |
Optional expression matrix for calculating co-expression for
the reference, with the same organization as |
nPerm |
Number of permutations for assessing statistical significance. |
geneNames |
Optional vector indicating a subset of genes in |
dopar |
Logical indicating whether to process features in parallel. Make sure to register a parallel backend first. |
scale |
Logical indicating whether to scale CCD by the number of gene pairs. |
A data.table with columns for group name, CCD, and p-value.
getRefCor()
, calcDeltaCCD()
, plotHeatmap()
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