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Functions for Genotype by (Marker+Trait) data


A genotype-by-(marker+trait) table is made of 2 two-way tables: a genotype-by-marker table and a genotype-by-trait table (of genotypic or phenotypic values). Therefore, in addition to the functions for 1) a genotype by trait table and 2) a genotype by marker table.


The following snapshot is part of a barley QTL mapping dataset, in which the rows are 145 barley doubled haploids, and the columns are 127 genetic markers plus 22 agronomic/quality traits. Only part of the data is shown. The highlighted columns are traits, and the un-highlighted are markers. (Note that the milling values are indicated by "-99" in this case, although it can be anything, preferably leaving them empty if it is an MS Excel file.)



We will use this dataset to illustrate the following functions for this type of data: