Description Usage Arguments Value Author(s)
Function to generate genotype probabilities across the genome for a given DSPR dataset. This function is most useful for those wishing to fit their own models.
1 | DSPRgenos(design, phenotype.dat, id.col, output = "list")
|
design |
a character string. For inbred RIL designs: 'inbredA', 'inbredB'. For cross designs: AAcross, BBcross, or 'ABcross'. A and B refer to the pA and pB set of DSPR RILs. |
phenotype.dat |
|
id.col |
a character string identifying the name of the column containing unique ids for the samples. e.g. for an inbred design, the patRIL column can be used as the id. |
output |
a character string identifying the preferred format for the output of genolist. Options are 'list' or 'array'. Default is 'list'. |
A list containing:
genolist |
a list containing the matrix of additive genotype probabilities at each position in the genome. The list is in the same order as the list of positions described below. Column names are the different DSPR haplotypes and row names are the unique ids provided in id.col. Alternatively, if output='array', the output is a 3 dimensional array [samples, haplotypes, positions]. Haplotypes and samples are named while positions are in the order of the list of positions described below. |
positions |
a |
phenotype |
the phenotype.dat |
Elizabeth King (kingeg@missouri.edu)
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