dupli: Small data set to illustrate 'SNP.rm.duplicates'

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Small data set to illustrate SNP.rm.duplicates

Description

The SNPs in this data frame are as follows:

SNP 1.

Unduplicated SNP

SNPs 2a and 2b.

Two duplicated SNPs with identical alleles

SNPs 3a and 3b.

Two duplicated SNPs with swapped alleles

SNPs 4a and 4b.

Two duplicated SNPs with flipped reference strand

SNPs 5a and 5b.

Two duplicated SNPs with swapped alleles and flipped reference strand

SNPs 6a and 6b.

Two duplicated SNPs with incompatible alleles

SNPs 7a and 7b.

Two duplicated SNPs including one monomorphic SNP (one allele set to "0")

SNPs 8a, 8b and 8c.

Three duplicated SNPs

SNPs 9a, 9b and 9c.

Three duplicated SNPs with incompatible alleles

Usage

 data(dupli) 

Format

There are three data objects in the dataset:

dupli.gen

Genotype matrix

dupli.ped

Data frame containing all variables corresponding to a .fam file

dupli.bim

Data frame containing all variables corresponding to a .bim file

See Also

SNP.rm.duplicates

Examples

data(dupli)
x <- as.bed.matrix(dupli.gen, fam = dupli.ped, bim = dupli.bim)

gaston documentation built on May 29, 2024, 7:33 a.m.