pheno2geno (version 1.4.0)

create.population: Create a population object

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.

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.

Details

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

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

# NOT RUN {
	### 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)
# }