getDyads: Getter only for all dyads (child and one parent)

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

Getter only for all dyads (child and one parent)

Description

Wrapper function for genDataGetPart that returns a subset of the data containing only dyads (where the child and only one parent have genetic data), i.e., not triads.

Usage

getDyads(
  data.in = stop("No data given!", call. = FALSE),
  file.out = "my_data_onlyDyads",
  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_onlyDyads").
dir.out	The path to the directory where the output files will be saved (default: ".", the current directory).
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 Sept. 11, 2024, 7:13 p.m.