causalASCEND

Causal ASCEND (Ancestral Scalable Causal discovEry via iNherited Descent) infers ancestral relations among downstream molecular variables, such as gene expression, when a layer of upstream variables, such as genotypes, is known to precede them.

BiocManager::install("causalASCEND")   # once accepted by Bioconductor
library(causalASCEND)
sim <- simulateTwoTier(n = 2000, nBackground = 20, nForeground = 15,
    r2 = 0.7, sparsity = 0.9, pCross = 0.2, effect = 0.9, seed = 1)
res <- ascend(sim$background, sim$foreground)
ancestralEdges(res)

Input: two matrices (features in rows, samples in columns), two SummarizedExperiment objects, or a MultiAssayExperiment (ascendMultiAssay()). See vignette("causalASCEND").

Reference: Asiedu S, Watson D. Causal ASCEND: scalable two-tier causal discovery on high-dimensional multi-omics data.