BBB_NMP_pl_subset: Example for "pl" format specification

In RZooRoH: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes

Example for "pl" format specification

Description

A dataset containing real genotype likelihoods in phred scores for 1,000 SNPs. The data is available for ten individuals and the first 1,000 SNPs on chromosome 1. The data corresponds to a low-fold sequencing experiment. There are three columns per individuals (for genotypes 00, 01 and 11).

Usage

BBB_NMP_pl_subset

Format

A data frame with 1,000 rows and 35 variables:

chr

The chromosome number

marker_name

The marker id

pos

The position of the marker

allele1

The name of the first marker allele

allele2

The name of the second marker allele

id1_pl1

The AA phred likelihood for the first individual

id1_pl2

The AB phred likelihood for the first individual

id1_pl3

The BB phred likelihood for the first individual

id2_pl1

The AA phred likelihood for the second individual

id2_pl2

The AB phred likelihood for the second individual

id2_pl3

The BB phred likelihood for the second individual

id3_pl1, id3_pl2, id3_pl3, id4_pl1, id4_pl2, id4_pl3, id5_pl1, id5_pl2, id5_pl3, id6_pl1, id6_pl2, id6_pl3, id7_pl1, id7_pl2, id7_pl3, id8_pl1, id8_pl2, id8_pl3, id9_pl1, id9_pl2, id9_pl3, id10_pl1, id10_pl2, id10_pl3

The phred likelihoods for the other individuals

RZooRoH documentation built on Oct. 27, 2023, 9:07 a.m.