empty_onemap_obj: Produce empty object to avoid code break. Function for...
In onemap: Construction of Genetic Maps in Experimental Crosses

empty_onemap_obj

R Documentation

Produce empty object to avoid code break. Function for internal purpose.

Produce empty object to avoid code break. Function for internal purpose.

empty_onemap_obj(vcf, P1, P2, cross)

`vcf`	object of class vcfR
`P1`	character with parent 1 ID
`P2`	character with parent 2 ID
`cross`	type of cross. Must be one of: `"outcross"` for full-sibs; `"f2 intercross"` for an F2 intercross progeny; `"f2 backcross"`; `"ri self"` for recombinant inbred lines by self-mating; or `"ri sib"` for recombinant inbred lines by sib-mating.

An empty 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.