13.5 lm_map statements

limit recombination fractions L

This statement is optional and places lower and upper bounds on the estimated recombination fractions of the map. For markers that are separated ny little or no recombination, the MCEM algorithm may yield estimated recombination fractions of zero which could lead to a severe bias in the results. As a safeguard against such events, this statement places a lower bound L and an upper bound 0.5 - L on the estimated recombination fractions of the map.

output maps gender [averaged] [specific]

This statement specifies the type of map to be estimated. The default behavior is to select both options, which instructs lm_map to automatically compute the likelihood ratio test statistic for testing the null hypothesis of a sex-averaged map.

use MCEM and SA for maximization

If the statement `use MCEM only for maximization' is replaced by this statement, lm_map will attempt to refine its MCEM based estimate of the MLE by performing additional SA steps.

set genotyping error rate E

When the statement `set map estimation with mistyping' is used, the genotype observations are assumed to have an associated error rate. This statement allows for the specification of the `mistyping' rate.

set SA curvature iterations I

An estimate of the curvature of the likelihood is needed to initiate the SA algorithm. This statement tells lm_map to use at least I MCMC realizations to estimate the curvature of the likelihood. The curvature is only estimated once.

set SA ascent iterations I

lm_map will not initiate the SA algorithm with a step that decreases the likelihood. This statement tells lm_map to use at least I MCMC realizations to determine whether a proposed first step increases the likelihood.

set SA gradient iterations I

If SA is initiated, this tells lm_map to use at least I MCMC realizations to estimate the gradient of the likelihood. An estimate of the gradient is needed for each SA step.

set SA convergence R

The SA algorithm is terminated, if all recombination fraction updates are within R of their previous values. In addition, the maximum possible runtime for the SA algorithm is proportional to the total runtime of the MCEM algorithm.

set map estimation [with] [with no] mistyping

This statement can be used to specify whether or not errors were made during the observation of genotype. If `with no' is selected, the gentypes are assumed to have been observed without error. If `with' is selected, the genotype observations are assumed to have some error associated with them, which can be specified using the `set genotyping error rate' statement.

set LRT stat iterations I

This statement tells lm_map to use at least I MCMC realizations to estimate the LRT statistics. If only one option is used in `output maps gender ...', then the estimated LRT statistic compares the MLE to the initial map. Otherwise, two LRT statistics are estimated. The first compares the MLE of the sex-averaged map to the initial sex-averaged map, while the second compares the MLE of the sex-specific map to the MLE of sex-averaged map.

compute estimates I times

This statement tells lm_map to conduct its entire analysis I times, and to report the map with the highest likelihood. While this statement offers some protection against convergence to local modes, the default value is 1.