p.dlm.ls: Discrete Local Maxima approximate p-value.

In ASSET: An R package for subset-based association analysis of heterogeneous traits and subtypes

Description

Function to obtain Discrete Local Maxima based estimates of pvalues for z-scores maximized over subsets (of traits or subtypes), with possible restrictions and weights. Should not be called directly. See details.

Usage

p.dlm.ls(t.vec, k, search, side, sizes=rep(1, k), 
      sub.def=NULL, sub.args=NULL, wt.def=NULL, wt.args=NULL)

Arguments

t.vec	Numeric vector of (positive) points for which to calculate p-values, i.e. general observed Z-max values. No default.
k	Integer (currently less than 30). The number of studies (traits) or subtypes being analyzed. No default.
search	0, 1 or 2. Search option, with 0 indicating subtype analysis, 1 and 2 denote one-sided and two-sided subset-search. No default.
side	Either 1 or 2. For two-tailed tests (where absolute values of Z-scores are maximized), side should be 2. For one-tailed tests side should be 1 (positive tail assumed). No default. Ignored when search is 2.
sizes	Sizes of equivalence classes of traits. By default, no two traits or studies are equivalent. This argument is for internal use.
sub.def	A function to restrict subsets, e.g., order restrictions in subtype analysis. Should accept a subset (a logical vector of size k) as its first argument and should return TRUE if the subset satisfies restrictions and FALSE otherwise. Default is NULL implying all (2^k - 1) subsets are considered in the maximum.
sub.args	Other arguments to be passed to sub.def as list. Default is NULL (i.e. none).
wt.def	A function that gives weight of one subset with respect to another. Should accept two subsets as first two argumets and return a single positive weight. Default NULL. Currently this option is not implemented and the argument is ignored.
wt.args	Other arguments to be passed to wt.def as a list . Default NULL. Currently ignored.

Details

The function is vectorized to handle blocks of SNPs at a time. Currently weight options are ignored. This is a helper function that is called internally by h.traits and h.types and should not be called directly. The arguments of this function that have defaults, can be customized using the argument pval.args in h.traits and h.types.

Value

A numeric vector of estimated p-values.

ASSET documentation built on May 2, 2019, 5:46 p.m.