pheno2geno (version 1.4.0)

scan.qtls: Scan qtls

Description

Scanning population data for qtls for use in cross.saturate function.

Usage

scan.qtls(population,map=c("genetic","physical"), env, epistasis = c("scan","ignore"),
  step=0.1,verbose=FALSE)

Arguments

population

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

map

Which map (from ones stored in population$maps) should be used fo assigning chromosomes on the created map

env

Vector of environmental conditions - for each of the individuals specifies a condition. Ignored if missing.

epistasis

Should the two markers epistasis be scanned for. It is a heavy procedure!

step

Maximum distance (in cM) between positions at which the genotype probabilities are calculated, though for step = 0, probabilities are calculated only at the marker locations. See calc.genoprob for more information .

verbose

Be verbose.

Value

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

Details

This function takes care about qtl scan that is used by cross.saturate function. It was made separated function, since process itself takes a long time and before running cross.saturate function one should run markerPlacementPlot to assess the optimal threshold.

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

# NOT RUN {
  
# }
# NOT RUN {
  data(testPopulation)
  testPopulation <- scan.qtls(testPopulation,verbose=TRUE,map="genetic",step=0)
  
# }