gwSnpScreen-methods {GGtools} | R Documentation |
genome-wide test for association between SNP and phenotype
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.
data(hmceuB36.2021) objects("package:GGBase") g1 = gwSnpScreen( genesym("CPNE1"), hmceuB36.2021, chrnum(20) ) g1 plot(g1)