Description Usage Arguments Details Value Author(s) See Also Examples
Create a de novo genetic map from offspring phenotype data stored in a population object
1 2 3 4 | cross.denovo(population, n.chr, map=c("none", "genetic", "physical"),
comparisonMethod = c(sumMajorityCorrelation, majorityCorrelation, meanCorrelation,
majorityOfMarkers), assignFunction=c(assignMaximumNoConflicts, assignMaximum),
reOrder=TRUE, use.orderMarkers=FALSE, verbose=FALSE, debugMode=0, ...)
|
population |
An object of class |
n.chr |
Number of chromosomes expected on the map. |
map |
Which map ( from ones stored in population$maps) should be used for assigning chromosomes on the created map. If none is selected - assigning is not performed. |
comparisonMethod |
Method used to compare chromosomes from the new map to the original ones while assigning:
|
assignFunction |
function used to assign chromosomes on the created map, in both cases for every chromosome from the new map, original chromosome with maximal score is assigned, but if one of the original chromosomes is assigned to more then one of new ones:
|
reOrder |
if TRUE, cross object is returned, FALSE - vector showing how chromosomes should be assigned |
use.orderMarkers |
should markers on the newly created map be ordered using R/qtl orderMarkers funtion |
verbose |
be verbose |
debugMode |
1: Print our checks, 2: print additional time information |
... |
parameters passed directly to the |
cross.denovo function creates new genetic map using genotypes simulated by generate.biomarkers
function. Then it uses information provided by user to
assign number to newly created chromosomes.
When reordering this will produce an object of class cross
, otherwise (reOrder=FALSE)
a chromosomes assignment vector (See assignChrToMarkers
) is produced which can be used to manual reorder the markers.
Konrad Zych k.zych@rug.nl, Danny Arends Danny.Arends@gmail.com Maintainer: Konrad Zych k.zych@rug.nl
reorganizeMarkersWithin
- Apply new ordering on the cross object usign ordering vector.
assignChrToMarkers
- Create ordering vector from chromosome assignment vector.
cross.saturate
- Saturate existing map.
reduceChromosomesNumber
- Number of routines to reduce number of chromosomes of cross object.
generate.biomarkers
- Creating genotype markers out of gene expression data.
1 2 3 | data(testPopulation)
cross <- cross.denovo(testPopulation,n.chr=5,verbose=TRUE,map="genetic",
comparisonMethod=sumMajorityCorrelation, use.orderMarkers=FALSE)
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