create.population: Create a population object

In KonradZych/phenotypes2genotypes: High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains

Description

Create a new population object from phenotype data already loaded in the R environment

Usage

  create.population(offspringPhenotypes, founders, foundersGroups, offspringGenotypes,
  mapsGenetic, mapsPhysical, populationType=c("riself", "f2", "bc", "risib"),
  noWarn=FALSE, verbose=FALSE, debugMode=0)

Arguments

offspringPhenotypes	A matrix that contains the phenotype data measured on the offspring (required).
founders	A matrix that contains the phenotype data measured on the founders (required).
foundersGroups	When multiple measurement for the founders are present this is used to group the founders. The format is a matrix that contains the phenotype data measured on the (required).
offspringGenotypes	Matrix containing any known offspring genotype data (optional).
mapsGenetic	Matrix containing a known genetic map (optional).
mapsPhysical	Matrix containing a known physical map (optional).
populationType	Type of population the expression data was obtained from: riself - Recombinant inbred line by selfing. f2 - F2 cross. bc - Back cross. risib - Recombinant inbred line by sibling mating.
noWarn	If TRUE, no warnings will be produced.
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

When all required information is provided an object of class population is returned.

Value

An object of class population. This is a complex object containing all the information needed for the entire pheno2geno analysis. It's structure looks like below (depending on which optional information was supplied):

• $offspring - Section in the object which contains all data related to the offspring:

  • $phenotypes - Offspring phenotype data, stored as a numeric matrix, Rows: phenotypes, Columns: individuals.

  • $genotypes - (Optional) Offspring genotype data:

    • $real - The original data when a known genetic map is provided by the user - numeric matrix, Rows: markers, Columns: individuals.

    • $simulated - Simulated genetic map produced by generate.biomarkers from phenotype data - numeric matrix, Rows: markers, Columns: individuals.

• $founders - Section in the object which contains all data related to the founders:

  • $phenotypes - Founders phenotype data, stored as a numeric matrix, Rows: phenotypes, Columns: individuals.

  • $groups - Groups a founder belong to when replicates are available, storad as a vector of 0s and 1s, specifying per column which founder phenotype data belongs to which group.

  • $RP - Results from the t.test or RankProd analysis on the founders phenotype data, by find.diff.expressed.

• $maps - Section in the object which contains all data related to maps:

  • $genetic Genetic map, stored as a numeric matrix, Rows: markers, 2 Columns [1] Chromosome, [2] Position on chromosome in cM.

  • $physical Physical map, stored as anumeric matrix, Rows: markers, 2 Columns [1] Chromosome , [2] Position on chromosome in Mbp.

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.

• add.to.population - Adding data to an existing population object.

Examples

	### simulating data
	population <- fake.population()
	offspring <- population$offspring$phenotypes
	founders <- population$founders$phenotypes
	founders_groups <- population$founders$groups
	population <- create.population(offspring,founders,founders_groups)

KonradZych/phenotypes2genotypes documentation built on May 30, 2019, 2:45 p.m.