AncestryMapper: Assigning Ancestry Based on Population References

Assigns genetic ancestry to an individual and studies relationships between local and global populations.

Install the latest version of this package by entering the following in R:
install.packages("AncestryMapper")
AuthorTiago R Magalhaes, Eoghan T O'Halloran
Date of publication2016-09-28 19:28:04
MaintainerEoghan T O'Halloran <eoghan.ohalloran2@mail.dcu.ie>
LicenseGPL-2
Version2.0

View on CRAN

Files

inst
inst/extdata
inst/extdata/Demo.tped
inst/extdata/All-00.bed
inst/extdata/Prep.fam
inst/extdata/Example.phenoValues
inst/extdata/Example.phenoId
inst/extdata/Demo.tfam
inst/extdata/Prep.bed
inst/extdata/IndRm
inst/extdata/CorPheno
inst/extdata/HGDP_References.txt
inst/extdata/All-00.fam
inst/extdata/HGDP_500SNPs.ped
inst/extdata/All-00.bim
inst/extdata/Demo.snplist
inst/extdata/Prep.bim
inst/doc
inst/doc/AncestryMapper2.0.Rmd
inst/doc/AncestryMapper2.0.R
inst/doc/AncestryMapper_tutorial_2.0.pdf
inst/doc/AncestryMapper2.0.html
NAMESPACE
NEWS
data
data/medoidArithmetic_Han.South.China_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Burmese_Chaubey2010_1000_Illumina.rda
data/medoidArithmetic_Yoruba_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Dyak_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Bedouin_HGDP_1000_Illumina.rda
data/MinMaxFreq.rda
data/medoidArithmetic_Maasai_HapMap_1000_Affymetrix.rda
data/medoidArithmetic_Papuan_HGDP_1000_Illumina.rda
data/medoidArithmetic_Han.Beijing_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Mari_Raghavan2013_1000_Illumina.rda
data/medoidArithmetic_Romanian_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Mandenka_HGDP_1000_Illumina.rda
data/medoidArithmetic_Spanish_1000.Genomes_1000_WG.rda
data/medoidArithmetic_South.Italian_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Tunisian_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Yizu_HGDP_1000_Illumina.rda
data/medoidArithmetic_Bulgarian_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_Lezgi_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Ethiopian.Jew_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Kalash_HGDP_1000_Illumina.rda
data/medoidArithmetic_Temuan_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Polish_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Ukrainian_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_Yemeni.Jewish_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Tujia_HGDP_1000_Illumina.rda
data/medoidArithmetic_Uzbek_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Kazakh_Raghavan2013_1000_Illumina.rda
data/medoidArithmetic_Lahu_HGDP_1000_Illumina.rda
data/medoidArithmetic_Puerto.Rican_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Estonian_Raghavan2013_1000_Illumina.rda
data/medoidArithmetic_Tuscan_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Lithuanian_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Bantu_HGDP_1000_Illumina.rda
data/medoidArithmetic_Jehai_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Chuvash_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Tamil_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Gujarati_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Evenki_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_Nganassan_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_Irish_UCD_1000_Illumina.rda
data/medoidArithmetic_Mamanwa_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Cypriot_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Balochi_HGDP_1000_Illumina.rda
data/medoidArithmetic_Peruvian_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Iranian_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Mozabite_HGDP_1000_Illumina.rda
data/medoidArithmetic_Australian.Aborigine_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Sardinian_HGDP_1000_Illumina.rda
data/medoidArithmetic_Hungarian_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Armenian_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_Selkup_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_Euro.Utah_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Miaozu_HGDP_1000_Illumina.rda
data/medoidArithmetic_Makrani_HGDP_1000_Illumina.rda
data/medoidArithmetic_Surui_HGDP_1000_Illumina.rda
data/medoidArithmetic_Burusho_HGDP_1000_Illumina.rda
data/medoidArithmetic_Saudi_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Nogai_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_Esan_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Emirati_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Palestinian_HGDP_1000_Illumina.rda
data/medoidArithmetic_Turkmen_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_Finnish_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Ossetian_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_Chukchi_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_Altai_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_Pima_HGDP_1000_Illumina.rda
data/medoidArithmetic_Tuvan_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_Kinh_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Mexican_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Luhya_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Manobo_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Moroccan.Jewish_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Bulgarian_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_French_HGDP_1000_Illumina.rda
data/medoidArithmetic_Basque_HGDP_1000_Illumina.rda
data/medoidArithmetic_Georgian_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Kyrgyz_Raghavan2013_1000_Illumina.rda
data/medoidArithmetic_Balkar_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_Turkish_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Oroqen_HGDP_1000_Illumina.rda
data/medoidArithmetic_Barbadan_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Gujarati_HapMap_1000_Affymetrix.rda
data/medoidArithmetic_Iraqi.Jewish_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Norwegian_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Tu_HGDP_1000_Illumina.rda
data/medoidArithmetic_San.Khomani_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Buryat_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_Gambian_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Khmer_HGDP_1000_Illumina.rda
data/medoidArithmetic_Ashkenazi_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Yakut_HGDP_1000_Illumina.rda
data/medoidArithmetic_Sandawe_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Hazara_HGDP_1000_Illumina.rda
data/medoidArithmetic_Brahui_HGDP_1000_Illumina.rda
data/medoidArithmetic_Syrian_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Sindhi_HGDP_1000_Illumina.rda
data/medoidArithmetic_Druze_HGDP_1000_Illumina.rda
data/medoidArithmetic_Chechen_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_Bidayuh_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Uygur_HGDP_1000_Illumina.rda
data/medoidArithmetic_Fijian_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Han.Dallas_HapMap_1000_Affymetrix.rda
data/medoidArithmetic_Ethiopian_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Pathan_HGDP_1000_Illumina.rda
data/medoidArithmetic_Greek_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Moroccan_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Yemeni_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Mordovin_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_North.Italian_HGDP_1000_Illumina.rda
data/medoidArithmetic_Egyptian_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Na-Dene_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_Eastern.Greenlander_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_Adygei_HGDP_1000_Illumina.rda
data/medoidArithmetic_Colombian_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Western.Greenlander_Rasmussen2010_1000_Illumina.rda
data/medoidArithmetic_East.Sicilian_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Tibetan_Wuren2014_1000_Affymetrix.rda
data/medoidArithmetic_PNG.Southern.Highlands_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Dai_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Russian_HGDP_1000_Illumina.rda
data/medoidArithmetic_Punjabi_1000.Genomes_1000_WG.rda
data/medoidArithmetic_West.Sicilian_Hellenthal2014_1000_Illumina.rda
data/medoidArithmetic_Sephardic_Behar2010_1000_Illumina.rda
data/medoidArithmetic_Japanese_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Orcadian_HGDP_1000_Illumina.rda
data/medoidArithmetic_Karitiana_HGDP_1000_Illumina.rda
data/medoidArithmetic_Kumyk_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_Bengali_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Mongolian_HGDP_1000_Illumina.rda
data/medoidArithmetic_Abkhaz_Yunusbayev2011_1000_Illumina.rda
data/medoidArithmetic_British_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Biaka-Py_HGDP_1000_Illumina.rda
data/medoidArithmetic_Mende_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Polynesian_Reich2011_1000_Illumina.rda
data/medoidArithmetic_Melanesian_HGDP_1000_Illumina.rda
data/medoidArithmetic_She_HGDP_1000_Illumina.rda
data/medoidArithmetic_Telugu_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Han_HGDP_1000_Illumina.rda
data/medoidArithmetic_Maya_HGDP_1000_Illumina.rda
data/medoidArithmetic_Khaskassian_Fedorova2013_1000_Illumina.rda
data/medoidArithmetic_African.American_1000.Genomes_1000_WG.rda
data/medoidArithmetic_Mbuti-Py_HGDP_1000_Illumina.rda
data/medoidArithmetic_Dravidian_Reich2011_1000_Illumina.rda
R
R/R_CreateMedoids.R R/Plot_AncestryMapper.R R/CorphenoMaker.R R/R_CalculateAMIds.R R/R_AMids_distanceToArithmeticMedoids_SingleMedoids.R
vignettes
vignettes/index.html
vignettes/AncestryMapper2.0.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/arithmeticRefsMedoids.Rd man/AncestryMapper2.0-package.Rd man/calculateAMids.Rd man/refAdd.Rd man/plotAMids.Rd man/calculateAMidsArith.Rd man/createMedoid.Rd man/MinMaxFreq.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.