example_genotypes: Filtered Genotypes For The Simulated Data

In bahlolab/XIBD: Identity-by-Descent Analysis of the Human Genome

Description

Processed raw genotype data with the parameter settings as in the Vignette and following topbot alterations.

Usage

example_genotypes

Format

A list of two objects named pedigree and genotypes:

1. pedigree is a data frame with the following information:

   1. Family ID

   2. Isolate ID

   3. Paternal ID. This is not used by XIBD and is set to zero.

   4. Maternal ID. This is not used by XIBD and is set to zero.

   5. Gender - 1 for male and 2 for female

   6. Affection status of individuals. This is set to 2 and is ignored by XIBD IBD inference.

2. genotypes is a data frame with the first 11 columns:

   1. Chromosome

   2. SNP identifier

   3. Genetic map distance

   4. Base-pair position

   5. Population allele frequency

   6. Condition SNP number

   7. Conditional probability Pr(ba)

   8. Conditional probability Pr(bA)

   9. Conditional probability Pr(Ba)

   10. Conditional probability Pr(BA)

   11. Allele frequency of conditioned SNP

   where each row describes a single SNP. Columns 12 onwards contain the genotype data for each individual, where a single column corresponds to a single individual. These columns are labeled with merged family IDs and individual IDs separated by a slash symbol (/).

bahlolab/XIBD documentation built on May 11, 2019, 5:24 p.m.