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Options for the SNPRelate LD-Pruning Backend

Source: R/ld.R
LdPruningOptions.Rd

Build a checked record of extra arguments for SNPRelate::snpgdsLDpruning(), the engine behind ldPruneByCorrelation(backend = "snprelate").

Usage

LdPruningOptions(...)

Arguments

...

Arguments for SNPRelate::snpgdsLDpruning() – in practice the window controls slide.max.bp and slide.max.n (pruning is greedy within a window, so the window bounds which pairs are ever compared), maf, missing.rate, remove.monosnp and num.thread. gdsobj, method, ld.threshold and verbose are supplied by pecotmr and refused. The temporary GDS pecotmr writes holds every sample and variant of X on one synthetic chromosome, so sample.id, snp.id and autosome.only are not meaningful selectors here.

Value

A MethodOptions record for ldPruneByCorrelation(methodArgs =).

See also

ldPruneByCorrelation

Examples

LdPruningOptions(slide.max.bp = 1e6)
#> <MethodOptions: ldPruning>
#>   forwarded to SNPRelate::snpgdsLDpruning()
#>   argument names checked against SNPRelate::snpgdsLDpruning()
#>   slide.max.bp           1e+06