Description Usage Arguments Details Value Author(s) See Also Examples
Scanning population data for qtls for use in cross.saturate function.
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population |
An object of class |
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 |
verbose |
Be verbose. |
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.
An object of class population
. See create.population
for details.
Konrad Zych k.zych@rug.nl, Danny Arends Danny.Arends@gmail.com Maintainer: Konrad Zych k.zych@rug.nl
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.
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data(testPopulation)
testPopulation <- scan.qtls(testPopulation,verbose=TRUE,map="genetic",step=0)
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