richNull {GGtools} | R Documentation

## 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

### 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.

### Value

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

### Author(s)

Vince Carey <stvjc@channing.harvard.edu>

[Package GGtools version 5.16.0 Index]