submapSummary: Submap summary

In genostats/Fantasio: Genetic Data Analyses in Presence of Inbreeding

Submap summary

Description

This function creates a summary on the submaps created.

Usage

submapSummary(submaps, a.threshold = 1)

Arguments

submaps	a list of submaps
a.threshold	the maximum value for a (default is 1)

Details

This function gives for each genotyped individual summary statistics about the calculations.

This function returns a dataframe with 13 columns :

- famid : family identifier

- id : individual identifier

- pheno : phenotype (1 non affected, 2 affected, 0 unknown)

- submaps : number of valid submaps (i.e. submaps with a < a.threshold)

- quality: percentage of valid submaps

- f_min: minimum f on valid submaps

- f_max: maximum f on valid submaps

- f_mean: mean f on valid submaps

- f_median: median f on valid submaps (recommended to estimate f)

- a_median: median a on valid submaps (recommended to estimate a)

- pLRT_median: median p-value of LRT tests on valid submaps

- inbred: a flag indicating if the individual is inbred (pLRT_median <0.05) or not

- pLRT_<0.05: number of valid submaps with a LRT having a p-value below 0.05

Value

this function returns a dataframe.

See Also

setSummary

genostats/Fantasio documentation built on Feb. 2, 2023, 5:28 p.m.