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Convert GBRS tsv genome probabilities to genoprobs format.

genoprobably.Rd

Converts GBRS-formatted TSV genotype probability files into a 3D array format compatible with qtl2, organized by tissue and sample, optionally saves the result as an RDS file

Usage

genoprobably(
  outfile = "./gbrs_interpolated_genoprobs.rds",
  gbrsFileLoc,
  tissues = c(),
  gridFile = gridfile,
  save = "sr"
)

Arguments

outfile

File path to save the resulting genopbrobs list. Defaults to "gbrs_interpolated_genoprobs.rds".

gbrsFileLoc

File path to where the GBRS files are located.

tissues

Character vector of tissue names. These should match substrings in the GBRS file names. if empty, defaults fo "a".

gridFile

Either a data frame or file path to the genome grid used to assign marker names. Default is 75K grid loaded with the package.

save

Character. Determines output behavior: "sr" to save and return, "so" to save only, "ro" to return only. Default is "sr".

Value

A named list of 3D genotype probability arrays (one per tissue), formatted for use with qtl2.