richNull: bind metadata concerning SNP allele frequency and other...
In GGtools: software and data for analyses in genetics of gene expression

Description Usage Arguments Details Value Author(s)

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

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))
#

`...`	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

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.

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

Vince Carey <stvjc@channing.harvard.edu>

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.