convert_marker_dosages: Convert marker dosages to the basic types.

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description

Convert marker dosages to the basic types which hold the same information and for which linkage calculations can be performed.

Usage

convert_marker_dosages(dosage_matrix, outname, ploidy = 4, ploidy2 = NULL,
  parent1 = "P1", parent2 = "P2", marker_conversion_info = FALSE,
  log = NULL)

Arguments

dosage_matrix	An integer matrix with markers in rows and individuals in columns.
outname	output filename (deprecated for now)
ploidy	ploidy level of the plant species. If parents have different ploidy level, ploidy of parent1.
ploidy2	ploidy level of the second parent. NULL if both parents have the same ploidy level.
parent1	Character string specifying the first (usually maternal) parentname.
parent2	Character string specifying the second (usually paternal) parentname.
marker_conversion_info	Logical. Should marker conversion information be returned?
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

A modified dosage matrix. If marker_swap_info = TRUE, this function returns a list.

Examples

data("ALL_dosages")
conv<-convert_marker_dosages(dosage_matrix=ALL_dosages)

mdavy86/polymapR documentation built on May 25, 2019, 9:35 p.m.