Test All Cached Markers Fast method for performing single marker testing across all variants stored in the kalis::CacheHaplotypes

Test All Cached Markers Fast method for performing single marker testing across all variants stored in the kalis::CacheHaplotypes

Usage

TestCachedMarkers(
  y,
  A = NULL,
  from = 1L,
  to = kalis::L(),
  ploidy = 2L,
  model = "additive"
)

Arguments

y

a n x m matrix of m quantitative phenotypes (one phenotype / column)

A

a n x q matrix of q background covariates

from

a positive integer giving the index of the first variant in the cache that should be tested, default = 1L.

to

a positive integer giving the index of the last variant in the cache that should be tested, default = kalis::L(), the last variant.

ploidy

a positive integer giving the ploidy of the organisms whose haplotypes were cached, default = 2L.

model

a character in "additive", "recessive", or "dominant" giving the model of inheritance that should be tested, default = "additive"

Value

a data.frame of -log10 p-values. Each row corresponds to a variant tested (in order starting with the variant with index from) and each of the m columns corresponds to a phenotype provided in y (in the same order as the columns of y).