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).