cisSnpTests {GGtools} | R Documentation

## perform tests for eQTL cis to specified genes

### Description

perform tests for eQTL cis to specified genes

### Usage

    cisSnpTests(fmla, smls, radius, ...)

### Arguments

`fmla` | standard formula. LHS can be a GeneSet with AnnotationIdentifier geneIdType. RHS can be predictor formula component using variables in pData of `smls`
`smls` | instance of smlSet
`radius` | numeric value: number of bases up and downstream from probe CHRLOC to be examined for SNP
`...` | not in use

### Value

a list of cwSnpScreen instances

### Note

Getting SNP locations is slow for the first event while metadata are brought into scope. Subsequent calls are faster.

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

### Examples

    library(GSEABase)
    # two genes on chr 20
    gs1 = GeneSet(c("CPNE1", "ADA"), geneIdType = SymbolIdentifier())
    gs2 = gs1
    organism(gs2) = "Homo sapiens"
    geneIdType(gs2) = AnnotationIdentifier("illuminaHumanv1.db")
    if (!exists("hmceuB36.2021")) data(hmceuB36.2021)
    cc = cisSnpTests(gs2~male, hmceuB36.2021, radius=1e5)
    lapply(cc, function(x) length(p.value(x@.Data[[1]])))
    cc = cisSnpTests(gs2~male, hmceuB36.2021, radius=1e6)
    lapply(cc, function(x) length(p.value(x@.Data[[1]])))

[Package GGtools version 3.2.0 Index]