Calculate the difference between the clock correlation distances (CCDs), relative to a reference, for two groups of samples. Statistical significance is calculated using permutation of the samples that belong to either of those two groups.
Usage
calcDeltaCCD(
refCor,
emat,
groupVec,
groupNormal,
refEmat = NULL,
nPerm = 1000,
geneNames = NULL,
dopar = FALSE,
scale = FALSE
)
Arguments
- refCor
Correlation matrix to be used as the reference, such as comes from
getRefCor()
. Should contain Spearman correlation values.- emat
Matrix of expression values, where each row corresponds to a gene and each column corresponds to a sample. The rownames and colnames of
refCor
should be present in the rownames ofemat
. For the p-value calculation, it is important thatemat
include all measured genes, not just those inrefCor
.- groupVec
Vector indicating the group to which group each sample belongs. It's ok for groupVec to have more than two groups.
- groupNormal
Value indicating the group in groupVec that corresponds to normal or healthy. Other groups will be compared to this group.
- refEmat
Optional expression matrix for calculating co-expression for the reference, with the same organization as
emat
. Only used ifrefCor
is not provided.- nPerm
Number of permutations for assessing statistical significance.
- geneNames
Optional vector indicating a subset of genes in
refCor
,emat
, and/orrefEmat
to use for calculating the CCD.- dopar
Logical indicating whether to process features in parallel. Make sure to register a parallel backend first.
- scale
Logical indicating whether to use scaled CCDs to calculate difference.
Value
A data.table with columns for group 1, group 2, deltaCCD, and
p-value. In each row, the deltaCCD is the CCD of group 2 minus the CCD of
group 1, so group 1 corresponds to groupNormal
.