calc_q1

Pvalue

Fraction invalid scores of bestParentfit segtype

fracInvalid

bestfit

bestParentfit

Threshold P-value of bestParentfit segtype

Pvalue_threshold

a maximum threshold for the fracInvalid of the bestParentfit segtype
(with a larger fraction of invalid dosages in the F1 the q1 quality parameter will be set to 0)

fracInvalid_threshold

Calculate q1 quality score. q1 is a measure of the fit of selfit. 
It is based on Pvalue and the fraction of valid F1 scores. If either is below their 
threshold the q1 value is 0. Also, if bestParentfit is different from bestfit this indicates a segregation distortion.

Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>.

calc_q1: calc_q1 ***********************************************************

Description

Usage

Arguments