gwSnpScreen-methods {GGtools}R Documentation

genome-wide test for association between SNP and phenotype

Description

genome-wide test for association between SNP and phenotype

Methods

sym = "genesym", sms = "smlSet", cnum="cnumOrMissing"
sym is an instance of genesym class (typically just a wrapped character string giving a SYMBOL value for the expression annotation package in use, or a GeneSet instance, see below); sms is an integrative instance of smlSet containing snp.matrix genotype data in a list and coordinated expression data. Restriction of analysis to specific chromosomes can be accomplished by passing an instance of chrnum as the third argument.

The gwSnpScreen computes the snp.rhs.tests from snpMatrix for all snp against the specified expression phenotype.

If sym is an instance of the GSEABase GeneSet class, a list of gwSnpScreenResults is packaged in a multiGwSnpScreenResult instance.

Examples

data(hmceuB36.2021)
objects("package:GGBase")
g1 = gwSnpScreen( genesym("CPNE1"), hmceuB36.2021, chrnum(20) )
g1
plot(g1)

[Package GGtools version 2.0.2 Index]