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).