Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/cross.saturate.R
Saturating an existing genetic map using markers derived from phenotype data.
1 2 3 | cross.saturate(population, cross, map=c("genetic","physical"), placeUsing=c("qtl",
"correlation"), flagged = c("remove","warn","ignore"), threshold=3, chr, env,
use.orderMarkers=FALSE, verbose=FALSE, debugMode=0)
|
population |
An object of class |
cross |
An object of class |
map |
Which map should be used for comparison:
|
placeUsing |
How should the position of the new markers on the saturated map be determinated:
|
flagged |
How to handle the markers influenced by epistatic or environmental interactions:
|
threshold |
Specifies a threshold for the selection of new phenotype markers (see markerPlacementPlot). |
chr |
When specified the algorithm only saturates a subset of chromosomes. If not specified, all the chromosomes will be saturated. |
env |
Vector of environmental conditions - for each of the individuals specifies a condition. Ignored if missing. |
use.orderMarkers |
If true the algorithm (after initial saturation) performs an |
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. |
This function saturates an existing map with markers derived from the phenotype data provided inside either the cross or population object. A correlation matrix between those two sets of markers is made, and new markers are assigned to the 'optimal' location on the map.
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
reorganizeMarkersWithin
- Apply new ordering on the cross object usign ordering vector.
assignChrToMarkers
- Create ordering vector from chromosome assignment vector.
cross.denovo
- Create de novo genetic map or chromosome assignment vector.
reduceChromosomesNumber
- Functions to reduce the number of chromosomes in a cross object.
markerPlacementPlot
- Plot showing how many markers will be selected for map saturation with different thresholds.
1 2 | data(testPopulation)
cross <- cross.saturate(testPopulation,map="genetic",verbose=TRUE,debugMode=2)
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