Create a state.matrix.object to be used encode marker information in a form in which it can be used in subsequent calculations.
make.state.matrix(marker.frame, marker.distances, method="F2")n by k by q array. q is 3 for method="F2" and 2 for others methods. Each element encodes the probability of the allele state conditional on the marker states.
Actually, this is a misnomer. This is NOT
amarker.frame.object. Rather it is obtained by by call like
make.marker.numeric(marker.frame.object) (see
make.marker.numeric ) and it is coerced to
a matrix. It encodes marker allele states. One column is used for each
marker or pseudo-marker (basically a placeholder with all missing
values). The entries are in 1:6, if NA's are present, they are
recoded to 6. The columns are arranged in
linkage groups with presumed order reflected in the actual order of the
columns.
Distances between the markers in the 'lambda' metric. -log(lambda)/2 is the Haldance map distance. Linkage groups are separated by values of 0.0.
method = "F2" is the default, and "BC1", "RI.self", and "RI.sib" are other options. The assumed setup is as follows (strains are A and a):
| marker state | F2.code | BC.code | RI.code |
"AA" | 1 | 1 | 1 |
"Aa" | 2 | 2 | |
"aa" | 3 | 2 | |
"A-" (not aa) | 4 | ||
"a-" (not AA) | 5 | ||
"--" (unknown) | 6 | 6 | 6 |
Lander E.S. and Green P. (1987) Construction of multilocus genetic linkage maps in humans. Proceedings of the National Academy of Sciences of the United States of America, 84(8), 2363--7.
Jiang C. and Zeng Z-B. (1997) Mapping quantitative trait loci with dominant and missing markers in various crosses from tow inbred lines. Genetica 101, 47-58.