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.
magicFounderReconstruct(snp_dir, phenotypes = NULL, id = NULL)
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 |
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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. |
an object of type "MagicGen" or "MagicGenPhen".
# to be added...