add.to.population: Add additional data to a population object

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

Description

Add additional data to an existing population object. When adding data already present in the population objects the function will issue a warning.

Usage

  add.to.population(population, dataObject, dataType=c("founders",
  "offspring$phenotypes",  "founders$group", "offspring$genotypes",
  "maps$genetic","maps$physical","annotations"), verbose=FALSE,debugMode=0)

Arguments

population	An object of class population. See create.population for details.
dataObject	A matrix of data to be put into the population objects, or a list of matrices.
dataType	Specifies what kind of data dataObject contains, if dataObject is a list of matrices to add, dataType should be a list of the same length: founders - Founders phenotype. offspring$phenotypes - Offspring phenotype. founders$group - Specifying groups in founders phenotypes. offspring$genotypes - Offspring genotype. maps$genetic - Genetic map. maps$physical - Physical map. annotations - Annotations file.
verbose	Be verbose.
debugMode	Either use 1 or 2, this will modify the amount of information returned to the user. 1) Print out checks, 2) Print additional time information.

Details

This function inputs data into existing population object. It can input single matrix or list of matrices.

Value

An object of class population. See create.population for details.

Author(s)

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

See Also

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

• create.population - Create object of class population from data already in R environment.

• fake.population - Simulate basic population object for use in examples.

Examples

  population <- fake.population()
  offspring <- population$offspring$phenotypes
  founders <- population$founders$phenotypes
  founders_groups <- population$founders$groups
  maps_genetic <- population$maps$genetic
  population <- create.population(offspring,founders,founders_groups)
  population <- add.to.population(population,maps_genetic,"maps$genetic")

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