association.test.logistic.dosage {milorGWAS}

Mixed logistic regression for GWAS, using dosages

Description

Mixed logistic regression for GWAS, using dosages

Usage

association.test.logistic.dosage(
  filename,
  Y,
  X,
  K,
  beg,
  end,
  algorithm = c("amle", "offset"),
  eigenK,
  p = 0,
  n.cores = 1L,
  ...
)

Arguments

filename

Name of a dosage file

Y

phenotype vector. Default is column pheno of x@ped

X

A matrix of covariates (defaults to a column of ones for the intercept)

K

A genetic relationship matrix (or a list of such matrices)

beg

Index of the first SNP tested for association

end

Index of the last SNP tested for association

algorithm

Algorithm to use

eigenK

eigen decomposition of K (only if p > 0)

p

Number of principal components to include in the model

n.cores

number of cores to use

...

Additional parameter for gaston::logistic.mm.aireml

Details

Dosage files can be VCF files with 'DS' or 'GP' fields. It is also possible to use a file with columns 'id"', 'chr', 'pos', 'A1', 'A2', 'sample1', 'sample2', etc. These files should have a header with column names.

For more details refer to association.test.logistic and association.test.

Value

A data frame giving for each SNP the association statistics.

See Also

association.test.logistic, association.test