gp_overview function

gp_overview

Function to generate an overview of genotype probabilities across a population

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.

Returns

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)