richNull: bind metadata concerning SNP allele frequency and other aspects of optimized cis-eQTL association to an mcwBestCis instance

Description

bind metadata concerning SNP allele frequency and other aspects of optimized cis-eQTL association to an mcwBestCis instance, to allow conditional FDR computation

Usage

richNull(..., MAFlb = 0.01, npc = 10, radius = 250000, nperm = 1,  innerFilt = function(x) x, outerFilt = function(x) x)
meta.richNull(..., MAFlb=.01, npc=10, radius=250000, nperm=1, innerFilt=function(x)x, outerFilt=function(x)x) 
#
# internally:
#
#  bigfilt = function(z) 
#    outerFilt(MAFfilter(clipPCs(permEx(innerFilt(z)), 1:npc), lower=MAFlb))
#

Arguments

...

should provide bindings for smpack and chrnames, which will be used to obtain gene/probe locations; see getSS for information on smpack settings.

meta.richNull allows a vector of smpack values bound to smpackvec

MAFlb

lower bound on SNP MAF for null distribution evaluation

npc

number of expression principal components to be removed

radius

radius used for testing

nperm

This establishes how many permutations of expression against genotype will be performed for this process.

innerFilt

function immediately applied to generated smlSet instances

outerFilt

function applied to generated smlSet instances after clipPCs and MAFfilter are applied in that order

Value

richNull returns a list of nperm mcwBestCis instances with additional metadata bound in

Details

The purpose of richNull is to obtain realizations from the permutation distribution of cis-eQTL association statistics, binding information on the characteristics of the optimal results with the scores. This allows us to use conditioning with the realizations from the permutation distribution.