marker_data_summary: Summarize marker data

In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description

Gives a frequency table of different markertypes, relative frequency per markertype of incompatible offspring and the names of incompatible progeny.

Usage

marker_data_summary(dosage_matrix, ploidy = 4, pairing = c("random",
  "preferential"), parent1 = "P1", parent2 = "P2",
  progeny_incompat_cutoff = 0.1, verbose = TRUE, log = NULL)

Arguments

dosage_matrix	An integer matrix with markers in rows and individuals in columns.
ploidy	Integer. Ploidy of plant species.
pairing	Type of pairing. "random" or "preferential".
parent1	Name of first parent. Usually maternal parent.
parent2	Name of second parent. Usually paternal parent.
progeny_incompat_cutoff	The relative number of incompatible dosages per genotype that results in reporting this genotype as incompatible. Incompatible dosages are greater than maximum number of alleles than can be inherited or smaller than the minimum number of alleles that can be inherited.
verbose	Logical, by default TRUE - should intermediate messages be written to stout?
log	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

Returns a list containing the following components:

parental_info	frequency table of different markertypes. Names start with parentnames, and behind that the dosage score.
offspring_incompatible	relative frequency of incompatible offspring with same layout as parental_info.
progeny_incompatible	progeny names having incompatible dosage scores higher than threshold at progeny_incompat_cutoff.

Examples

data("ALL_dosages")
summary_list<-marker_data_summary(dosage_matrix = ALL_dosages)

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