find.mixups: Find sample mix-ups

In pheno2geno: High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains

Description

Finding possible sample mix-ups in the data.

Usage

  find.mixups(population,map=c("genetic","physical"),n.qtls=50,threshold=15,verbose=FALSE)

Arguments

population	An object of class population. See create.population for details.
map	Which map should be used to determine the ordering / positions of original markers.
n.qtls	Number of qtls that we use for scanning for mix-ups.
threshold	When an individual is not matching the expected genotype more the x % of the time. The individual should be considered as being a mix-up.
verbose	Be verbose.

Details

After scanning for the requested number of QTLs, each individual is checked if their genotype is matching the expected genotype. If an individuals expression value is not in the range of the expected genotype (mean - 3*sd, mean+3*sd), it's receives a penaltie. After which the individuals above the threshold are being printed with a warning about possible mix-up.

Value

An vector with for each individual a percentage that shows how many times an individual didn't match the expected genotype.

Author(s)

Konrad Zych [e-mail], Danny Arends [e-mail] Maintainer: Konrad Zych [e-mail]

See Also

• read.population - Load genotype, phenotype, genetic map data files into R environment into a population object.

• cross.denovo - Create de novo genetic map or vector showing how chromosomes should be assigned.

• cross.saturate - Saturate existing map.

• find.diff.expressed - Using Rank Product or student t-test analysis to select differentially expressed genes.

Examples

	data(testPopulation)
  scores <- find.mixups(testPopulation,map="genetic",n.qtls=10,threshold=5,verbose=FALSE)
  plot(scores[[2]])

pheno2geno documentation built on May 2, 2019, 6:35 a.m.