Description Details References
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 (across pairs of populations) statistics. Various plotting functions are also included to facilate vizualisation and interpretation of the results.
Package: | rehh |
Version: | 1.0 |
License: | GPL(>=2) |
Depends: | gplots , methods |
Index:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | 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
ies2rsb Compute Rsb (standardized ratio of
iES from two populations)
ihh2ihs Compute iHS (standardized iHH)
ihsplot Plot iHS over a genome
make.example.files Generate example input files
rsbplot Plot Rsb over a genome
scan_hh Computing EHH based statistics over
a whole chromosome
wgscan.cgu Whole genome scan results for the CGU
(Creole from Guadeloupe island)
wgscan.eut Whole genome scan results for a pool of
European taurine cattle
|
Gautier, M. and Vitalis, R. (2012). rehh: An R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics, accepted.
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