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]