addRef2GDS1KG: Add the information about the unrelated patients to the GDS...

In belleau/aicsPaper: Accurate Inference of Genetic Ancestry from Cancer Sequencing

Add the information about the unrelated patients to the GDS 1KG file

Description

This function adds the information about the unrelated patients to the GDS 1KG file. More specificaly, it creates the field sample.ref which as the value 1 when the sample is unrelated and the value 0 otherwise. The sample.ref is filled based on the information present in the input RDS file.

Usage

addRef2GDS1KG(fileNameGDS, filePart)

Arguments

fileNameGDS	a character string representing the path and file name of the GDS file that contains the 1KG information. The GDS file must contain the SNP information, the genotyping information and the pedigree information from 1000 Genomes. The extension of the file must be '.gds'.
filePart	a character string representing the path and file name of the RDS file that contains the information about the 1KG patients that are unrelated. The extension of the file must be '.rds'. The file must exists.

Value

None

Author(s)

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Examples

## Path to the demo pedigree file is located in this package
data.dir <- system.file("extdata", package="RAIDS")

## 1K GDS file
GDS_file <- file.path(data.dir, "1KG_Demo.gds")

belleau/aicsPaper documentation built on Aug. 4, 2022, 1:12 a.m.