compute_LD_blocks: Compute LD blocks
In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

compute_LD_blocks

R Documentation

Compute LD blocks

Compute LD blocks using snpClust.

compute_LD_blocks(
  x,
  stats = c("R.squared", "D.prime"),
  type = c("capushe", "bstick"),
  k.max = NULL,
  pct = 0.15,
  verbose = TRUE
)

`x`	either a genotype matrix of class `SnpMatrix`/`matrix` or a linkage disequilibrium matrix of class `dgCMatrix`. In the latter case the LD values are expected to be in [0,1]
`stats`	a character vector specifying the linkage disequilibrium measures to be calculated (using the `ld` function) when `x` is a genotype matrix. Only "R.squared" and "D.prime" are allowed, see Details.
`type`	model selection approach between slope heuristic (`"capushe"`) and broken stick approach (`"bstick"`)
`k.max`	maximum number of clusters that can be selected. Default to `NULL`, in which case it is set to `\min(\max(100, \frac{n}{\log(n)}), \frac{n}{2})` where `n` is the number of objects to be clustered for capushe and to `n` for the broken stick model
`pct`	minimum percentage of points for the plateau selection in capushe selection. See `DDSE` for further details
`verbose`	Print messages.