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).