find.bins: Allocate markers into bins

In BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

Description

Function to allocate markers with redundant information into bins. Within each bin, the pairwise recombination fraction between markers is zero.

Usage

find.bins(input.obj, exact = TRUE, ch = NULL)

Arguments

input.obj	an object of class onemap.
exact	logical. If TRUE, it only allocates markers with the exact same information into bins, including missing data; if FALSE, missing data are not considered when allocating markers. In the latter case, the marker with the lowest amount of missing data is taken as the representative marker on that bin.
ch	not used in this OneMap version. Chromosome for which the analysis should be performed. If NULL the analisys is performed for all chromosomes.

Value

An object of class onemap.bin, which is a list containing the following components:

bins	a list containing the bins. Each element of the list is a table whose lines indicate the name of the marker, the bin in which that particular marker was allocated and the percentage of missing data. The name of each element of the list corresponds to the marker with the lower amount of missing data among those on the bin
n.mar	total number of markers.
n.ind	number individuals
exact.search	logical; indicates if the search was performed with the argument exact=TRUE or exact=FALSE

Author(s)

Marcelo Mollinari, [e-mail]

See Also

create.data.bins

Examples

 ## Not run: 
  load(url("https://github.com/mmollina/data/raw/master/fake_big_data_f2.RData"))
  fake.big.data.f2
  (bins<-find.bins(fake.big.data.f2, exact=FALSE))
## End(Not run)

BatchMap documentation built on May 2, 2019, 3:45 p.m.