Changes in version 1.07 NEW FEATURES o Added scanone.assoc to perform genome wide association mapping. o Added calc.genoprob2 to run forward/backward algorithm once cluster parameters have been estimated. CHANGES o Fixed bug in assoc.map where the SDPs were not in the correct order. o Change assoc.map to use the Sanger VCF file rather than our own custom SNP file. Changes in version 1.06 NEW FEATURES o Added limited support for association mapping in Heterogeneous Stock mice. CHANGES o calc.genoprob.intensity Fixed bug in which probs were not written out on the X chromosome when mapping with males only. Changes in version 1.5.3 CHANGES o Added get.pgw() to allow users to get genome-wide p-values for LOD or -log10(p-values). Changes in version 1.5.0 CHANGES o Major changes to the signficance thresholds. We now produce separate autosomal and X chromosome thresholds. This means that the return value of scanone.perm() is a 2 column matrix (or array). The columns contain the autosomal and X Chr maximum statistics, respoectively. There is a new function called get.sig.thr() that implements the method of Broman et.al., Genetics, 2006 for calculating X chromosome thresholds. Changes in version 1.1.8 CHANGES o Fixed bug in X chromosome mapping. We now requrire sex as an additive covariate always. Changes in version 1.1.6 CHANGES o Moved MUGAExampleData and doMPI to "suggests" field in the DESCRIPTION file. o Changed haplotype reconstruction to work in Euclidean (X,Y) space. o Replaced mclust() with pamk() in initial genotype clustering at each marker. Pamk is faster and the EM algorithm seems to produce equivalent haplotype reconstructions. Changes in version 1.1.3 NEW FEATURES o Added support for HS rat haplotype reconstruction. o Added support parallel whole genome association mapping. Changes in version 0.99.1 NEW FEATURES o Added limited support for Heterogeneous Stock mice. o assoc.plot Added strain distribution patterns above the association mapping plot. CHANGES o rankZ Fixed bug relating to NA values. Changes in version 0.99.0 NEW FEATURES o read.vcf reads Sanger SNP VCF files. o assoc.map imputes Sanger SNPs onto DO genomes and performs association mapping. o Fixed bug in kinship.probs in which kinship per chromosome was not calculated correctly. o Improved gene layout algorithm in gene.plot. CHANGES o scanone returns p-values and -log10(p-values). o doqtl.plot plots either LOD or -log10(p-values).