getFullTriads: Getter for all full triads

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

Getter for all full triads

Description

Wrapper function for genDataGetPart that returns a subset of the data containing only full triads (where all, the child, the mother and the father have genetic data).

Usage

getFullTriads(
  data.in = stop("No data given!", call. = FALSE),
  file.out = "my_data_onlyTriads",
  dir.out = ".",
  overwrite = NULL
)

Arguments

data.in	The data object (in format as the output of genDataRead); note that the design of the data is assumed to be triad.
file.out	The base for the output filename (default: "my_data_onlyTriads").
dir.out	The path to the directory where the output files will be saved.
overwrite	Whether to overwrite the output files: if NULL (default), will prompt the user to give answer; set to TRUE, will automatically overwrite any existing files; and set to FALSE, will stop if the output files exist.

Value

A list object with three 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

• aux - a list with meta-data and important parameters.

This now contains only the selected subset of data.

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