Description: An S4 implementation of Eq. (3) and Eq. (7) by
Suggests: devtools, knitr, MASS, mda, nnet, pkgload, rmarkdown, rpart,
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

Suggests: caTools, devtools, knitr, MASS, mda, nnet, pkgload,
rmarkdown, ROCR, rpart, rprojroot, RUnit, testthat

Title: Univariate non-parametric two-sample test based on empirical
Description: Provides an R routine for a Cramer-von Mises type two sample test which is based on empirical Hankel transforms of the non-negative sample variables. The test is non-parametric and not distribution free. The exact value of the test statistic for univariate data as well as the p-value and the critical value are computed.

Description: Haplotype-Based Analysis of Association for genetic traits

Title: Multi-locus stepwise regression (MSR)

Description: The multi-locus stepwise regression (MSR) combines the advantages of stepwise regression and haplotype-based analysis. The MSR can be used to identify informative combinations of single nucleotide polymorphisms (SNPs) from unlinked SNPs (allele combinations) or SNPs within a chromosomal region (haplotypes).

Title: Inference of Chromosome-Length Haplotypes Using Genomic Data of
Description: Inference of chromosome-length haplotypes using a few haploid
gametes of an individual. The gamete genotype data may be generated from various platforms
including genotyping arrays and sequencing even with low-coverage. Hapi simply takes
genotype data of known hetSNPs in single gamete cells as input and report the high-resolution
haplotypes as well as confidence of each phased hetSNPs. The package also includes a module
allowing downstream analyses and visualization of identified crossovers in the gametes.
biocViews: SNP, GenomicVariation, Genetics, HiddenMarkovModel,

Package: Haplin
Type: Package
Title: Analyzing case-parent triad and/or case-control data with SNP
haplotypes
Version: 3.0.1
Date: 2009-05-25
Author: H�kon K. Gjessing
Maintainer: H�kon K. Gjessing <hakon.gjessing@fhi.no>
Depends: MASS, mgcv
Description: Haplin performs a genetic association analysis of
case-parent triad (trio) data with multiple markers. It can
also incorporate complete or incomplete control triads, for
instance independent control children. Estimation is based on
haplotypes, for instance SNP haplotypes, even though phase is
not known from the genetic data. Haplin estimates relative risk
(RR + conf.int.) and p-value associated with each haplotype. It
uses maximum likelihood estimation to make optimal use of data
from triads with missing genotypic data, for instance if some
SNPs has not been typed for some individuals. Haplin also
allows estimation of effects of maternal haplotypes,
particularly appropriate in perinatal epidemiology.
License: GPL (>= 2)
URL: http://www.uib.no/smis/gjessing/genetics/software/haplin/
Encoding: latin1
Packaged: 2009-05-27 08:33:08 UTC; hkgjess
Repository: CRAN
Date/Publication: 2009-05-27 08:58:57