calculateTFstoTargets: 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	calculateTFstoTargets(Mat, TFs, n.cores=1, mt_correction="bon=0.05")

`Mat`	gene by sample expression matrix after normalization and/or batch correction.
`TFs`	vector of gene names of the TFs of interest.
`n.cores`	number of cores to run in parallel.
`mt_correction`	string of the multiple-testing method to apply and the significance threshold, separated by an equals sign.

Calculates all pairwise correlations between a provided set of TFs using the distance correlation (dCor) statistic from the "energy" package. Runs in parallel on the specified number of cores. Applies the specified multiple testing correction.

The direction of the correlation is inferred using a t-test between the the values of the target for the top 25% and bottom 25% of the expression of the TF: -1 = negative 0 = unclear/other 1 = positive

Data frame with columns : Gene, Target, pval (dcor p.value), strength (dcor value), direction (-1, 0, 1)

getDirection

	Mat <- matrix(rnorm(1000), nrow=10);
	rownames(Mat) <- c("A", "B", "C", "D", "E",
			   "F", "G", "H", "I", "J")
	out <- calculateTFstoTargets(Mat, c("A", "B", "C", "D"), n.cores=1, mt_correction="fdr=0.2")