create_data_bins {onemap}

New dataset based on bins

Description

Creates a new dataset based on onemap_bin object

Usage

create_data_bins(input.obj, bins)

Arguments

input.obj

an object of class onemap.

bins

an object of class onemap_bin.

Details

Given a onemap_bin object, creates a new data set where the redundant markers are collapsed into bins and represented by the marker with the lower amount of missing data among those on the bin.

Value

An object of class onemap, i.e., a list with the following components:

geno

a matrix with integers indicating the genotypes read for each marker. Each column contains data for a marker and each row represents an individual.

n.ind

number of individuals.

n.mar

number of markers.

segr.type

a vector with the segregation type of each marker, as strings.

segr.type.num

a vector with the segregation type of each marker, represented in a simplified manner as integers, i.e. 1 corresponds to markers of type "A"; 2 corresponds to markers of type "B1.5"; 3 corresponds to markers of type "B2.6"; 4 corresponds to markers of type "B3.7"; 5 corresponds to markers of type "C.8"; 6 corresponds to markers of type "D1" and 7 corresponds to markers of type "D2". Markers for F2 intercrosses are coded as 1; all other crosses are left as NA.

input

the name of the input file.

n.phe

number of phenotypes.

pheno

a matrix with phenotypic values. Each column contains data for a trait and each row represents an individual.

error

matrix containing HMM emission probabilities

Author(s)

Marcelo Mollinari, [e-mail]

See Also

find_bins

Examples

  data("onemap_example_f2")
  (bins<-find_bins(onemap_example_f2, exact=FALSE))
  onemap_bins <- create_data_bins(onemap_example_f2, bins)