png_genotypes: Filtered Genotypes For The Papua New Guinea Dataset

In bahlolab/isoRelate: Identity-by-Descent Inference of Haploid Recombining Organisms

Description

Processed raw genotype data with the parameter settings as in the Vignette.

Usage

png_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 isoRelate and is set to zero.

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

   5. Multiplicity of infection - 1 for single infection and 2 for multiple infection

   6. Affection status of isolate. This is set to 2 and is ignored by isoRelate.

2. genotypes is a data frame with the first 5 columns:

   1. Chromosome

   2. SNP identifier

   3. Genetic map distance

   4. Base-pair position

   5. Population allele frequency

   where each row describes a single SNP. Columns 6 onwards contain the genotype data for each isolate, where a single column corresponds to a single isolate. These columns are labeled with merged family IDs and isolate IDs separated by a slash symbol (/).

bahlolab/isoRelate documentation built on May 11, 2019, 5:25 p.m.