Convert and process MUGA probabilities to qtl2 format

Converts MUGA genotyping final reports into a 3D array format compatible with qtl2, organized by tissue and sample, optionally saves the result as an RDS file

Usage

mugaprobs(
  type = "GM",
  covarLoc,
  covar_file,
  i.files,
  genoPrefix = "gm4qtl2",
  probsOut = "muga_interpolated_genoprobs.rds",
  saveDir = getwd(),
  tissues = c()
)

Arguments

type: One of c("GM", or "MM"); GigaMUGA or MegaMUGA. Default is "GM".
covarLoc: Location of covariate file.
covar_file: Covariate file including at minimum the sex (sex) and generation (ngen) of each sample, this needs to be a .csv file
i.files: Either a string of the directory where the chromosome specific genotype files are or a list of final report files to process - if passing the final report files they need to be either unzipped or in .gz format
genoPrefix: Prefix for the chromosome specific genotype files (excluding "_geno")
probsOut: File name to save probabilities, default is "muga_interpolated_genoprobs.rds".
saveDir: Directory to save genome probability object. Default is the current working directory.
tissues: List of tissues included in analysis. If left blank tissue will be set to "a".

Value

none