p.dlm: 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 p-values 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(t.vec, k, search, side, cor.def=NULL, cor.args=NULL, 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.
cor.def	A function with at least 3 arguments which calculates correlation between its first argument (a subset) and its second argument (subsets such as its neighbors). The third argument is the number of traits/subtypes and the function should return a vector of correlations with the neighbors. If NULL or a non-function value is specified, internal default functions for the corresponding search option are used.
cor.args	Other arguments to be passed to cor.def. These can include sample sizes and overlaps of different studies or subtypes and analysis option such as case-control or case-complement that affect the correlation structure. If cor.def is NULL, then ncase and ncntl must be specified in this list.
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 the weight of one subset with respect to another. Should accept two subsets as the first two arguments 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.

Examples

  # A function to define the correlations between a subset and its neighbors
  # Returned values should not exceed the value of 1
  cor.def <- function(subset, neighbors, k, ncase, ncntl) {
    n <- ncol(neighbors)
    mat <- matrix(subset, nrow=k, ncol=n, byrow=FALSE)
    cor <- (mat + neighbors)*(1:k)/(k^2)
    cor <- colSums(cor)
    cor <- cor/max(cor)
    dim(cor) <- c(n, 1)

    cor  
  }

  # Subset definition
  sub.def <- function(logicalVec) {
    # Only allow the cummulative subsets:
    # TRUE FALSE FALSE FALSE ...
    # TRUE TRUE FALSE FALSE ...
    # TRUE TRUE TRUE FALSE ...
    # etc
    sum <- sum(logicalVec)  
    ret <- all(logicalVec[1:sum])

    ret
  }

  k     <- 5
  t.vec <- 1:k

  p.dlm(t.vec, k, 1, 2, cor.def=cor.def, sub.def=sub.def,
         cor.args=list(ncase=rep(1000, k), ncntl=rep(1000,k)))

ASSET documentation built on Nov. 8, 2020, 5:20 p.m.