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]