inferMarkerPos: Find the best mapping position for a marker

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

inferMarkerPos Used to orient scaffolds or find markers that can fill gaps in a map.

Usage

inferMarkerPos(cross, marker.matrix, initial.geno.density = 20,
  final.step = 0.1, est.ci = FALSE, verbose = T, jitterMars = T,
  ...)

Arguments

cross	The QTL cross object.
marker.matrix	A numeric genotype matrix where the column names are markers and the row names are identical to the line IDs in the cross object
initial.geno.density	The initial distance between markers. Higher values speeds up the initial scan for the best chromosome. Corresponds to the min.distance argument of repPickMarkerSubset.
final.step	The density of pseudomarkers on the final scan. Corresponds to the step argument of calc.genoprob. Smaller values get more precision on estimates of marker position, but slow down the algorithm.
est.ci	Logical, should confidence intervals around the inferred position be estimated?
verbose	Logical, should updates be reported
jitterMars	logical, should a small amount of noise be added to the numeric genotype codes? In the case where a perfect association exists, LOD = inf. Setting this to TRUE makes all LOD scores numeric and finite.
...	Additional arguments passed to scanone. Cannot be "chr" or "method" as these are hard coded in the function.

Details

There are many methods to find the most likely position of a new marker. This approach attempts to speed up detection of the most likely position of a marker by using the haley-knott qtl scan to find the strongest correlation between markers in the genetic map and the numeric-coded genotypes of a new marker. This function can be used independently to order scaffolds during genome assembly, or to improve a genetic map. In the latter case, the results can be piped into fillGapsInMap to find the markers that will do the best job of increasing marker density. Once these markers are known it is best to go back and reconstruct the genetic map. However, if only a few markers are to be added, one could use qtl::addmarkers.

Value

A data frame with the most likely position of the marker.

Examples

library(qtlTools)
data(fake.bc)
cross<-fake.bc
## Not run: 
... more here ...

## End(Not run)

jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.