AncestryMapper: Assigning Ancestry Based on Population References

Share:

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

Author
Tiago R Magalhaes, Eoghan T O'Halloran
Date of publication
2016-09-28 19:28:04
Maintainer
Eoghan T O'Halloran <eoghan.ohalloran2@mail.dcu.ie>
License
GPL-2
Version
2.0

View on CRAN

Man pages

AncestryMapper2.0-package
Ancestry Mapper 2.0
arithmeticRefsMedoids
Object each reference file is assigned as it is loaded in or...
calculateAMids
Calculate genetic distances.
calculateAMidsArith
Calculate genetic distances.
createMedoid
Creates Ancestry Mapper Population Reference.
MinMaxFreq
Allele Variants for Demo SNPs According to dbSNP.
plotAMids
Visualises genetic distances.
refAdd
Add individuals to the CorPheno file.

Files in this package

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