dataACGT: Simulated Sperm-seq data A/C/G/T/NA encoded

In mccoy-lab/rhapsodi: R haploid sperm/oocyte data imputation

Simulated Sperm-seq data A/C/G/T/NA encoded

Description

Simulated Sperm-seq data from the generative model, with data A/C/G/T/NA encoded, with 50 gametes, 5000 beginning SNPs, 0.1 coverage, average recombination rate of 1, sequencing error rate of 0.005. Following filtering, there are 4136 hetSNPs. This data originated from the generative model with a random seed of 42, originally 0/1/NA encoded. Then dataACGT.R from the data-raw directory was run on the 0/1/NA encoded data to produce this A/C/G/T/NA encoded version. The first column is the SNP index positions the second column is the reference allele, the third the alternate allele, and the following 50 columns are the gamete genotypes which are encoded with A/C/G/T/NA.

Usage

dataACGT

Format

A dataframe with column names, 4136 rows, and 53 columns:

positions

positions, integer, SNP index pre-filtering for hetSNPs only

ref

ref, a character or string, the reference allele at that SNP

alt

alt, a character or string, the alternate allele at that SNP

gami_

gami_, A, C, G, T, or NA, the genotype at that SNP for gamete i

mccoy-lab/rhapsodi documentation built on July 27, 2022, 3:56 a.m.