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onemap (version 3.0.0)

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

Description

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

Usage

empty_onemap_obj(vcf, P1, P2, cross)

Value

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.

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.

Author

Cristiane Taniguti, chtaniguti@tamu.edu