empty_onemap_obj function

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

empty_onemap_obj(vcf, P1, P2, cross)

Arguments

• 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.

Returns

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.

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu