SnpMatrix object holding genotypes of
case subjects
control
SnpMatrix object holding genotypes
of control subjects
n.perm
number of permutations of case control
status required to generate permuted p value vectors.
The default, given by n.perm=0, is not to
permute.
pheno.perm
An alternative to specifying
n.perm is to supply a matrix of alternative
phenotypes, with each column relating to a different
permutation.
quiet
set TRUE to suppress the printing of
progress dots
Value
If n.perm=0, a vector of p values, one for each
SNP (each column in the case and control
objects. If n.perm>0, a matrix of p values, each
column representing the results of a different
permutation.
a LIST, use
data(for.exercise,package="snpStats")
case <- snps.10[subject.support$cc==1,]
control <- snps.10[subject.support$cc==0,]
summary(pairtest(case,control))