Using the dlmap package

The dlmap package represents the implementation of the DLMapping algorithm as described in [2]. DLMapping is a novel method of QTL mapping in a mixed model framework with separate detection and localization stages. The following vignette documents its usage through examples based on the datasets included in the package. The mixed model framework of the algorithm requires supplementary packages for model fitting. Two such packages, asreml and nlme, are supported through different versions of the package functions. The asreml functions are faster and more capable of handling complex models, but require a commercial license for ASReml. The other functions make use of the freely available R library nlme. We demonstrate below the usage of both asreml and lme functions to perform DLMapping. In the following sections, we present the steps required to perform a sample QTL analysis. First, we describe the DLMapping algorithm for those who are unfamiliar with its structure. Second, we describe the format for input files to dlmap. Third, we step through two examples using the datasets included in the package. In the first example, there is a single phenotypic observation for each genotype, and we compare the performance of three functions: composite interval mapping (CIM), and DLMapping using each of the mixed model packages (ASReml and nlme). Performing the analysis, interpreting the log files and output, and plotting results are all demonstrated in this section. In the second example, there is more than one phenotypic observation per genotype, and in this case only DLMapping using ASReml is applicable. The examples presented here do not cover every possible usage of the library functions, but clarify their basic implementation. Further detail can be found in the online help files for the package.