Usage
mvtests(phenotype, sets, stratum, data = sys.parent(), snp.data, rules = NULL, complete = TRUE, uncertain = FALSE, score = FALSE)
Arguments
phenotype
Either a factor (for a multinomial phenotype) or a matrix (for a
multivariate phenotype)
sets
A list of sets of SNPs to be tested against the phenotype
stratum
(Optional) a stratifying variable
data
A data frame in which phenotype and stratum reside. If
absent these are assumed to be in the parent frame and correctly
aligned with the rows of snp.data
snp.data
An object of class SnpMatrix containing the SNP data
rules
(Optional) A set of imputation rules. The function then carries out
tess on imputed SNPs
complete
If TRUE each test will use only subjects who have complete
data for the phenotype and all SNPs in the set to be tested. If
FALSE, then complete data for the phenotype is required, but
tests are based upon complete pairs of SNPs
uncertain
If TRUE, uncertain genotype calls will be used in the
tests (scored by their posterior expectations).
Otherwise such calls are treated as missing
score
If TRUE, the score vectors and their variance-covariance
matrices are saved in the output object for further processing