marker_data_summary {polymapR}

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)