Functions for the detection of footprints of selection on dense SNP data using Extended Homozygosity Haplotype (EHH) based tests. The package includes computation of EHH, iHS (within population) and Rsb or XP-EHH (across pairs of populations) statistics. Various plotting functions are also included to facilitate visualization and interpretation of the results.
|Author||Mathieu Gautier, Alexander Klassmann and Renaud Vitalis|
|Date of publication||2016-11-18 12:43:14|
|Maintainer||Mathieu Gautier <email@example.com>|
|License||GPL (>= 2)|
bifurcation.diagram: plot of an haplotype bifurcation diagram
calc_ehh: EHH and iHH computations at a given core SNP
calc_ehhs: EHHS and iES computations at a given core SNP
data2haplohh: Converting data into an object of class haplohh
distribplot: Distribution of standardized iHS or Rsb values
haplohh_cgu_bta12: Example of an 'haplohh' object
haplohh-class: Class '"haplohh"'
ies2rsb: Compute Rsb (standardized ratio of iES from two populations)
ies2xpehh: Compute xpEHH (standardized ratio of iES from two...
ihh2ihs: Compute iHS (standardized iHH)
ihsplot: Plot iHS over a genome
make.example.files: Creating example input files
rehh-package: Searching for footprints of selection using Haplotype...
rsbplot: Plot Rsb over a genome
scan_hh: Computing EHH based statistics over a whole chromosome
xpehhplot: Plot XPEHH over a genome