Pedigree analysis 👪

Author: Sonia Sarmiento

Description: Unlock and explore familial relationships in your dataset

Coding: all scripts are in R

Introduction

Welcome to the Pedigree Analysis Repository! Here you will find different R codes for analyzing familial relationships in your datasets. With our without pre-defined pedigree links, you can easily perform a variety of tasks and gain fruther insights into the relationships between individuals in your data. Whether you are working on a research project or just interested in exploring your own data, this repository is a great resource to have at your fingertips!

Some examples of what the scripts that are shown here are able to:

• Check any family links to correct when necessary
• Add any missing individuals to the pre-existing assigned families
• Make PED files for single or multiple trios to use, for instance, during pedigree phasing

Function 1: Checking family links

Ensure ped file relationship accuracy.

• Input: GDS file (from VCF), PED file
• Script: 1_Checking_family_links.R
• Output: Beta matrix, Correlation plots for each Family defined in PED File

Function 2: Plotting K0/K1 to solve undetermined relationships

K0/K1 plotting helps determine relatedness between individuals by plotting the number of alleles shared between two individuals (more specifically, no alleles shared - K0 - vs one allele shared - K1).

• Input: GDS file (from VCF), PED file
• Script: 2_IBD_Analysis.R
• Output: K0/k1 plots

To decipher relationships from K0/K1 graphs, this paper is crucial: Hill and Weir 2011

Function 3: Adding new individuals into the pedigree

Expand your pedigree with new individuals using this R code for checking relationships with existing families.

• Input: GDS file (from VCF), PED file, list of individuals you want to add
• Script: 3_Adding_individuals_to_pedigree.R
• Output: Beta matrix correlation plots with additional individuals

Function 4: Creating PED files with a focus individual

Create PED files considered a specific individual as focal. Specifically, close relationships are considered for how many trios as specified, prioritizing parental relationships and then grandparents, offspring, siblings and finally grandkids.

• Input: List of individuals, main PED file specifying all relationships
• Script: 4_Outputting_PED_files.R
• Output: PED files of focus individual (focus individual specified in the title)