create_data_bins function

New dataset based on bins

Creates a new dataset based on onemap_bin object

create_data_bins(input.obj, bins)

Arguments

• input.obj: an object of class onemap.
• bins: an object of class onemap_bin.

Returns

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

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.

Examples

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

See Also

find_bins

Author(s)

Marcelo Mollinari, mmollina@usp.br