Package: rehh 3.2.2
Alexander Klassmann
rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests
Population genetic data such as 'Single Nucleotide Polymorphisms' (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are included to facilitate visualization and interpretation of these statistics.
Authors:
rehh_3.2.2.tar.gz
rehh_3.2.2.tar.gz(r-4.5-noble)rehh_3.2.2.tar.gz(r-4.4-noble)
rehh_3.2.2.tgz(r-4.4-emscripten)rehh_3.2.2.tgz(r-4.3-emscripten)
rehh.pdf |rehh.html✨
rehh/json (API)
NEWS
# Install 'rehh' in R: |
install.packages('rehh', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://gitlab.com/oneoverx/rehh
- haplohh_cgu_bta12 - Example of an 'haplohh' object
Last updated 3 years agofrom:8352ae4f74. Checks:OK: 1 NOTE: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 02 2024 |
R-4.5-linux-x86_64 | NOTE | Dec 02 2024 |
Exports:as.newickcalc_candidate_regionscalc_ehhcalc_ehhscalc_furcationcalc_haplencalc_pairwise_haplencalc_region_statscalc_sfs_testschr.namedata2haplohhdistribplotextract_regionsfreqbinplothap.nameshaplohaplohh2sweepfinderies2xpehhihh2ihsines2rsbmake.example.filesmanhattanplotmrk.namesnhapnmrkpositionsremove.example.filesscan_hhscan_hh_fullupdate_haplohh
Dependencies:rehh.data