magicFounderReconstruct: Calculate MAGIC founder genotype probabilities

In tavareshugo/MagicHelpR: QTL mapping in Arabidopsis MAGIC lines

Description

This function calls the function 'happy.hbrem::happy()' to calculate the probability matrix of descent from each founder of the MAGIC lines at each marker SNP.

Usage

magicFounderReconstruct(snp_dir, phenotypes = NULL, id = NULL)

Arguments

snp_dir	directory with all genotype files. The function will be looking for files named "all_chr.MAGIC.happy.data", "all_chr.MAGIC.happy.map", "all_chr.MAGIC.happy.alleles", "founder_genotypes.tsv" and "magic_genotypes.tsv". All these files can be created with either the tidyArabMagic or downloadArabMagic functions.
phenotypes	a data.frame with phenotypes and with one of the columns being the MAGIC line IDs. This is set to NULL by default, which returns a 'MagicGen' object with no phenotypes included.
id	the name of the variable with IDs in the data.frame passed to 'phenotypes' argument. This is set to NULL by default, which returns a 'MagicGen' object with no phenotypes included.

Value

an object of type "MagicGen" or "MagicGenPhen".

Examples

# to be added...

tavareshugo/MagicHelpR documentation built on May 4, 2020, 3:01 p.m.