AncestryMapper: Assigning Ancestry Based on Population References

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

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

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

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