marker_data_summary: Summarize marker data

In polymapR: Linkage Analysis in Outcrossing Polyploids

Summarize marker data

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,
  ploidy2 = NULL,
  pairing = c("random", "preferential"),
  parent1 = "P1",
  parent2 = "P2",
  progeny_incompat_cutoff = 0.1,
  verbose = TRUE,
  shortform = FALSE,
  log = NULL
)

Arguments

dosage_matrix	An integer matrix with markers in rows and individuals in columns.
ploidy	Integer. Ploidy of parent 1, and .
ploidy2	Ploidy of parent 2, by default NULL, as it is assumed ploidy2 equals ploidy.
pairing	Type of pairing. "random" or "preferential".
parent1	Column name of first parent. Usually maternal parent.
parent2	Column 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?
shortform	Logical, by default FALSE. Returns only a shortened output with parental dosage summary, used internally by some functions.
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	Rate of incompatible ("impossible") marker scores (given as percentages of the total number of observed marker scores per marker class)
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, ploidy = 4)

polymapR documentation built on Nov. 5, 2023, 1:09 a.m.