View source: R/combine_onemap.R
combine_onemap | R Documentation |
Merge two or more OneMap datasets from the same cross type. Creates an
object of class onemap
.
combine_onemap(...)
... |
Two or more |
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.
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 |
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
|
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. |
Gabriel R A Margarido, gramarga@gmail.com
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.
read_onemap
and
read_mapmaker
.
data("onemap_example_out") data("vcf_example_out") combined_data <- combine_onemap(onemap_example_out, vcf_example_out)
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