convertToPhenot: Convert a genotype allele dataset to a phenotype dataset

In aleczwart/PolyPatEx: Paternity Exclusion in Autopolyploid Species

Description

Convert a 'genotypic' dataset (marker dosages known) to a 'phenotypic' dataset (marker dosages not known, unique alleles appear only once in each allele set).

Usage

convertToPhenot(adata)

Arguments

adata

data frame: a genotypic allele dataset.

Details

In the terminology used by the PolyPatEx package, a 'genotypic' allele dataset is one where marker dosages are known, hence any locus at which fewer than p (the ploidy) alleles are detected is incomplete (and subsequently ignored by the genotype-specific routines in this package). A 'phenotypic' allele dataset is one where marker dosages are not known, hence individual alleles appear only once in an allele set, and a complete allele set can contain between 1 and p alleles.

convertToPhenot converts a genotypic dataset to a phenotypic dataset, simply by removing any allele duplicates from each allele set. This is probably not something many will want to do, since one loses considerable information in the process...

Value

A data frame, containing the phenotypic form of the original genotypic dataset.

Author(s)

Alexander Zwart (alec.zwart at csiro.au)

Examples

## Using the example dataset 'FR_Genotype':
data(FR_Genotype)

## Since we did not load this dataset using inputData(), we must
## first process it with preprocessData() before doing anything
## else:
gData <- preprocessData(FR_Genotype,
                        numLoci=7,
                        ploidy=4,
                        dataType="genotype",
                        dioecious=TRUE,
                        mothersOnly=TRUE)

head(gData)  ## Checked and Cleaned version of FR_Genotype

pData <- convertToPhenot(gData)

head(pData)

aleczwart/PolyPatEx documentation built on May 11, 2019, 11:23 p.m.