combine_onemap {onemap}

Combine OneMap datasets

Description

Merge two or more OneMap datasets from the same cross type. Creates an object of class onemap.

Usage

combine_onemap(...)

Arguments

...

Two or more onemap dataset objects of the same cross type.

Details

Given a set of OneMap datasets, all from the same cross type (full-sib, backcross, F2 intercross or recombinant inbred lines obtained by self- or sib-mating), merges marker and phenotype information to create a single onemap object.

If sample IDs are present in all datasets (the standard new format), not all individuals need to be genotyped in all datasets - the merged dataset will contain all available information, with missing data elsewhere. If sample IDs are missing in at least one dataset, it is required that all datasets have the same number of individuals, and it is assumed that they are arranged in the same order in every dataset.

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

a string indicating that this is a combined dataset.

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)

Gabriel R A Margarido, [e-mail]

References

Lincoln, S. E., Daly, M. J. and Lander, E. S. (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. A Whitehead Institute for Biomedical Research Technical Report.

Wu, R., Ma, C.-X., Painter, I. and Zeng, Z.-B. (2002) Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theoretical Population Biology 61: 349-363.

See Also

read_onemap and read_mapmaker.

Examples

    
    data("onemap_example_out")
    data("vcf_example_out")
    combined_data <- combine_onemap(onemap_example_out, vcf_example_out)