gp_overview {polymapR}

gp_overview

Description

Function to generate an overview of genotype probabilities across a population

Usage

gp_overview(probgeno_df, cutoff = 0.7, alpha = 0.1)

Arguments

probgeno_df

A data frame as read from the scores file produced by function saveMarkerModels of R package fitPoly, or equivalently, a data frame containing the following columns:

SampleName

Name of the sample (individual)

MarkerName

Name of the marker

P0

Probabilities of dosage score '0'

P1...

Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)

maxP

Maximum genotype probability identified for a particular individual and marker combination

maxgeno

Most probable dosage for a particular individual and marker combination

geno

Most probable dosage for a particular individual and marker combination, if maxP exceeds a user-defined threshold (e.g. 0.9), otherwise NA

cutoff

a filtering threshold, by default 0.7, to identify individuals with more than alpha non-missing (maximum) genotype probabilities falling below this cut-off. In other words, by using this default settings (cutoff = 0.7 and alpha = 0.1), you require that 90 in one of the possible genotype dosage classes. This can help identify problematic individuals with many examples of diffuse genotype calls. Lowering the threshold allows more diffuse calls to be accepted.

alpha

Option to specify the quantile of an individuals' scores that will be used to test against cutoff, by default 0.1.

Value

a list with the following elements:

probgeno_df

Input data, filtered based on chosen cutoff

population_overview

data.frame containing summary statistics of each individual's genotyping scores

Examples

## Not run: 
data("gp_df")
gp_overview(gp_df)

## End(Not run)