get_stats_multiallele {cape} | R Documentation |
Perform linear regression on multi-allele markers.
Description
This function performs the multi-allele version of
linear regression. It is used in singlescan
and one_singlescanDO
. It performs marker-by-marker
linear regressions for each trait and adjusts for covariates.
It collects parameters from the linear models and returns
for downstream use.
Usage
get_stats_multiallele(phenotype, genotype, covar_table, ph_family, ref_col)
Arguments
phenotype |
A phenotype vector |
genotype |
genotypes of the marker being tested. If this is a vector, it will be converted into a one-column matrix. If it is a matrix, each column represents an allele, and each row represents an individual. |
covar_table |
The covariate matrix, with each covariate in a column, and each individual in a row. |
ph_family |
a character string for a description of the error distribution. Can be either "gaussian" or "binomial" |
ref_col |
The column belonging to the reference allele. The reference allele is removed from the genotype matrix so that the matrix is linearly independent. There are only n-1 degrees of freedom in the genotype matrix, where n is the number of alleles. |
Value
a list with "stats", "pval", "score" stats is a matrix holding the t statistics and slopes (beta coefficients) from the linear model. pval holds the p value for the marker overall and score holds the test statistic for the marker overall.