Description Usage Arguments Value See Also Examples
The class of object generated from sim.mpcross
and the format input to functions to construct linkage maps for multi-parent crosses. Basic constructor - takes required R objects and formats as an mpcross object.
1 | mpcross(founders, finals, pedigree, id, fid)
|
founders |
Matrix of founder genotypes |
finals |
Matrix of final genotypes |
pedigree |
Cross pedigree |
id |
Vector of numeric IDs for lines (which rows in pedigree are observed) |
fid |
Vector of founder IDs |
Let n.founders be the number of founders (either 4 or 8); n.finals be the number of final RILs genotyped; and n.mrk be the number of markers genotyped. Then
founders |
Founder genotypes - a matrix with dimensions n.founders x n.mrk. Row names of the matrix should be lines names; Column names should be marker names |
finals |
Final genotypes - a matrix with dimensions n.finals x n.mrk. Row names of the matrix should be line name; column names should be marker names. |
id |
Vector of final IDs with length n.finals |
fid |
Vector of founder IDs with length n.founders |
pedigree |
Numeric pedigree with 3 columns - mother, father, ID |
pheno |
Phenotypic data |
Optional components:
map |
Linkage map - either from which data was generated in |
ibd |
IBD genotypes from founders if data has been generated from |
qtlgeno |
Genotypes at QTL if data has been generated from |
rf |
Recombination fractions if data has been analyzed with |
lg |
Linkage groups if data has been analyzed with |
1 2 3 4 5 |
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