polymapR (version 1.1.1)

check_maxP: check your dataset's maxP distribution

Description

Function to assess the distribution of maximum genotype probabilities (maxP), if these are available. The function plots a violin graph showing the distribution of the samples' maxP.

Usage

check_maxP(probgeno_df)

Arguments

probgeno_df

A data frame as read from the scores file produced by function saveMarkerModels of R package fitPoly, or alternatively, 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 offspring 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

Value

This function does not return any value, is simply a visualisation tool to help assess data quality.

Examples

# NOT RUN {
data("gp_df")
check_maxP(gp_df)
# }