bqtl (version 1.0-7)

make.state.matrix: 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

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):

lccc{ marker state F2.code BC.code RI.code "AA" 1 1 1 "

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.

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.