convert_polyorigin: Create diaQTL input files from PolyOrigin output

In jendelman/diaQTL: QTL Analysis in Diallel Populations

Create diaQTL input files from PolyOrigin output

Description

Create diaQTL input files from PolyOrigin output

Usage

convert_polyorigin(
  filename,
  mapfile = NULL,
  remove.outliers = TRUE,
  outstem = ""
)

Arguments

filename	Name of polyancestry file
mapfile	Optional name of CSV file containing the physical map (marker, chrom, bp)
remove.outliers	Should offspring flagged as outliers be removed (default is TRUE)
outstem	prefix for output filenames

Details

Creates the pedigree (diaQTL_pedfile.csv) and genotype (diaQTL_genofile.csv) input files needed for read_data from the polyancestry output file generated by the PolyOrigin software. PolyOrigin outputs a genetic map in cM. To add a physical map in bp, use the option mapfile. The input file needed for phased_parents (diaQTL_parents.csv) is also created.

jendelman/diaQTL documentation built on Jan. 27, 2024, 6:39 a.m.