R: Calculate delta clock correlation distance.

calcDeltaCCD {deltaccd}

R Documentation

Calculate delta clock correlation distance.

Description

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 of `emat`. For the p-value calculation, it is important that `emat` include all measured genes, not just those in `refCor`.
`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 if `refCor` is not provided.
`nPerm`	Number of permutations for assessing statistical significance.
`geneNames`	Optional vector indicating a subset of genes in `refCor`, `emat`, and/or `refEmat` 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.

Examples

set.seed(35813)

refCor = getRefCor()
deltaCcdResult = calcDeltaCCD(
  refCor, GSE19188$emat, GSE19188$groupVec, 'healthy', nPerm = 100)