calculateConditionalCors: Calculate gene-gene correlations with dCor
In tallulandrews/scTarNet: Single-cell Targetted Network Inference

Description Usage Arguments Details Value See Also Examples

Calculates gene-gene correlations for a set of TFs to all genes in the genome using the dCor statistic from the "energy" package.

1	calculateConditionalCors(Mat, TFs, Dep, n.cores=1, threshold.interaction=0.01, bidirectional=TRUE, threshold.indirect=0.5, exclude.indirect=TRUE)

`Mat`	gene by sample expression matrix after normalization and/or batch correction.
`TFs`	vector of gene names of the TFs of interest.
`Dep`	output from calculateTFstoTargets
`n.cores`	number of cores to run in parallel.
`threshold.interaction`	threshold for calling pair of correlations as a TF-TF interaction.
`bidirectional`	whether TF-TF interactions must be bidirection. (see Details)
`threshold.indirect`	threshold for calling a correlation as indirect.
`exclude.indirect`	whether to remove indirect interactions from "Adj"

For each trio of two TFs (A, B) and a common target gene (T), calculates the conditional distance correlations:

pdCor(A, T | B) and pdCor(B, T | A)

if either of these are approximately zero (pdCor < threshold.indirect*original dCor) then infers an indirect interaction: pdCor(A, T | B) < T_indir * dCor(A, T) => A -> B -> T pdCor(B, T | A) < T_indir * dCor(B, T) => B -> A -> T

Indirect interactions are optionally removed from the dCor adjacency matrix.

if the conditional correlations are more than threshold.interaction bigger than original, then infers a TF-TF interaction: pdCor(A, T | B) > (1 + T_inter)*dCor(A, T) => A + B -> T pdCor(B, T | A) > (1 + T_inter)*dCor(B, T) => A + B -> T

if 'bidirectional' is TRUE then both of the above must be true to call a TF-TF interaction. TF-TF interaction trios are saved to a dataframe and returned.

Runs in parallel as specified by n.cores.

A list of two dataframe: Dep : the input TF to Target dataframe with indirect interaction removed or as provided (as specified with exclude.indirect) Int : a dataframe of TF-TF interactions with columns: TF1, TF2, Target

calculateTFstoTargets

	Mat <- matrix(rnorm(1000), nrow=10);
	rownames(Mat) <- c("A", "B", "C", "D", "E",
			   "F", "G", "H", "I", "J")
	Dep <- calculateTFstoTargets(Mat, c("A", "B", "C", "D"), n.cores=1, mt_correction="fdr=2")
	out <- calculateConditionalCors(Mat, c("A", "B", "C", "D"), Dep, n.cores=1, threshold.indirect=0.2, threshold.interaction=0.1, exclude.indirect=FALSE)