GenWin: Spline Based Window Boundaries for Genomic Analyses

Defines window or bin boundaries for the analysis of genomic data. Boundaries are based on the inflection points of a cubic smoothing spline fitted to the raw data. Along with defining boundaries, a technique to evaluate results obtained from unequally-sized windows is provided. Applications are particularly pertinent for, though not limited to, genome scans for selection based on variability between populations (e.g. using Wright's fixations index, Fst, which measures variability in subpopulations relative to the total population).

Author
Timothy M. Beissinger <beissinger@ucdavis.edu>
Date of publication
2014-09-26 16:51:09
Maintainer
Timothy M. Beissinger <beissinger@ucdavis.edu>
License
MIT + file LICENSE
Version
0.1

View on CRAN

Man pages

chr6
Maize Fst Data
splineAnalyze
Spline-based window analysis

Files in this package

GenWin
GenWin/NAMESPACE
GenWin/data
GenWin/data/chr6.RData
GenWin/R
GenWin/R/chr6-data.R
GenWin/R/spline_analyze.R
GenWin/MD5
GenWin/DESCRIPTION
GenWin/man
GenWin/man/chr6.Rd
GenWin/man/splineAnalyze.Rd
GenWin/LICENSE