Package: TRAMPR
Title: TRFLP Analysis and Matching Package for R
Version: 1.0-2
Author: Rich FitzJohn & Ian Dickie
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
License: GPL v2
Depends: R (>= 2.4)
Description: TRAMPR is an R package for matching terminal restriction
fragment length polymorphism (TRFLP) profiles between unknown
samples and a database of knowns.  TRAMPR facilitates analysis
of many unknown profiles at once, and provides tools for
working directly with electrophoresis output through to
generating summaries suitable for community analyses with R's
rich set of statistical functions.  TRAMPR also resolves the
issues of multiple TRFLP profiles within a species, and shared
TRFLP profiles across species.
Packaged: Mon Nov 20 12:28:40 2006; FitzJohnR

Package: TRAMPR
Title: TRFLP Analysis and Matching Package for R
Version: 1.0-4
Author: Rich FitzJohn & Ian Dickie
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
License: GPL v2
Depends: R (>= 2.4)
Description: TRAMPR is an R package for matching terminal restriction
fragment length polymorphism (TRFLP) profiles between unknown
samples and a database of knowns.  TRAMPR facilitates analysis
of many unknown profiles at once, and provides tools for
working directly with electrophoresis output through to
generating summaries suitable for community analyses with R's
rich set of statistical functions.  TRAMPR also resolves the
issues of multiple TRFLP profiles within a species, and shared
TRFLP profiles across species.
Packaged: Tue Jun  5 09:31:39 2007; fitzjohnr

database of known samples.  TRAMPR facilitates analysis of
statistical functions.  TRAMPR also resolves the issues of

Maintainer: Lam Opal Huang <opal.huang@mail.mcgill.ca>
Description: Transmission Ratio Distortion (TRD) is a genetic phenomenon where two alleles from either parent are not transmitted to the offspring at the Mendelian 1:1 ratio. Occurrence of TRD in general population can lead to false inflation or attenuation of association signals in case populations. Therefore, it is necessary to adjust for TRD in model fitting of case populations. This package uses models such as loglinear model (Weinberg 1998), augmented loglinear model (Huang 2014), and tests such as TDT (Spielman 1993), augmented TDT (Labbe 2013), on simulated or real datasets. This package has a simulation function which generates a population that is under the influence of TRD, and samples a sub-population, which can serve as the dataset to fit a loglinear model or to perform a TDT. Real dataset with the same data structure as described in the help file of the function 'll' can also be used in the loglinear model and the TDT functions. No real dataset is included in this package.