ldweight_edges: Include linkage disequilibrium information in the network.
In martini: GWAS Incorporating Networks

Description Usage Arguments Value Examples

Include linkage disequilibrium information in the SNP network. The weight of the edges will be lower the higher the linkage is.

1	ldweight_edges(net, ld, method = "inverse")

`net`	A SNP network.
`ld`	A `dsCMatrix` or `dgCMatrix` containing linkage disequilibrium measures, like the output of `ld`.
`method`	How to incorporate linkage-disequilibrium values into the network.

An copy of net where the edges weighted according to linkage disequilibrium.

ld <- snpStats::ld(minigwas[['genotypes']], depth = 2, stats = "R.squared")
# don't weight edges for which LD cannot be calculated
ld[is.na(ld)] <- 0
gi <- get_GI_network(minigwas, snpMapping = minisnpMapping, ppi = minippi)
ldGi <- ldweight_edges(gi, ld)