make.state.matrix {bqtl}

Create state.matrix.object

Description

Create a state.matrix.object to be used encode marker information in a form in which it can be used in subsequent calculations.

Usage

make.state.matrix(marker.frame, marker.distances, method="F2")

Arguments

marker.frame

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.

marker.distances

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

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

Value

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.

Note

It might have been better to design this array so that the third subscript moves fastest. In large problems, the current structure may involve excessive memory access.

References

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.