f.convert.matrix.ff: Converting Haplin-formatted matrix into the new format

In Haplin: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes

Converting Haplin-formatted matrix into the new format

Description

Internal function for converting an R matrix object into the new format of data used in Haplin. The output is the same as from genDataRead.

Usage

f.convert.matrix.ff(
  data = stop("You must give the data to convert!", call. = FALSE),
  n.vars = stop("You must explicitly give the number of columns with covariates!",
    call. = FALSE),
  cov.header,
  gen.levels
)

Arguments

data	A character matrix (NB: it's assumed that this matrix contains genotypes and covariate data, if any; i.e., as if it was a table read in from a haplin-formatted file).
n.vars	Number of columns with covariate variables - if the data does not contain covariates, give 0 explicitly.
cov.header	Optional; if there are covariates in the data, you can give their names explicitly here. Otherwise, dummy names will be created.
gen.levels	Optional; a vector with all the possible values for alleles in the genotype part of data. If not given, these will be assessed from the given data.

Value

A list object with two elements:

• cov.data - a data.frame with covariate data (if available in the input file)

• gen.data - a list with chunks of the genetic data; the data is divided column-wise, using 10,000 columns per chunk; each element of this list is a ff matrix

Haplin documentation built on May 20, 2022, 5:07 p.m.