AncestryMapper2.0-package: Ancestry Mapper 2.0

In AncestryMapper: Assigning Ancestry Based on Population References

Description

Package computes the genetic distance, defined as the euclidean distance amongst a sample set of individuals and any number of human population references. The package allows for the visualisation of the relationship of sample individuals to the reference populations, thus permitting the user to assess the relationship of individuals to different geographic groupings.

Package comes with pre-loaded with toy data and toy references from various sources comprising 158 global populations.

Additional and full Population References can be downloaded from:

http://bit.ly/1OUstDP

Details

Package:	AncestryMapper
Type:	Package
Version:	2.0
Date:	2016-08-??
License:	None
LazyLoad:	yes

Author(s)

Eoghan T. O'Halloran ,Tiago R. Magalh\~aes, Darren J. Fitzpatrick

Maintainer: Eoghan T. O'Halloran <[e-mail]>

References

Magalh\~aes et al, 2012 PLOS One accepted.

See Also

image dist

Examples

## Not run: 
library(AncestryMapper)
Refs <- system.file ("data", package = "AncestryMapper")

tpeds <- system.file ("extdata", package = "AncestryMapper")

Corpheno <- system.file ("extdata", "CorPheno", package =
"AncestryMapper")

All00Frq <- system.file ("data", "MinMaxFreq.rda", package = "AncestryMapper")

genetic.distance <- calculateAMidsArith(pathTotpeds = tpeds,
                                         NameOut = "Example",
                                         pathToAriMedoids = Refs,
                                         pathAll00 = All00Frq)

plotAMids(AMids = genetic.distance, phenoFile = Corpheno, columnPlot = "I")
## End(Not run)

Example output

[1] "Abkhaz.Yunusbayev2011 Finished"
[1] "Adygei.HGDP Finished"
[1] "African.American.1000.Genomes Finished"
[1] "Altai.Rasmussen2010 Finished"
[1] "Armenian.Yunusbayev2011 Finished"
[1] "Ashkenazi.Behar2010 Finished"
[1] "Australian.Aborigine.Reich2011 Finished"
[1] "Balkar.Yunusbayev2011 Finished"
[1] "Balochi.HGDP Finished"
[1] "Bantu.HGDP Finished"
[1] "Barbadan.1000.Genomes Finished"
[1] "Basque.HGDP Finished"
[1] "Bedouin.HGDP Finished"
[1] "Bengali.1000.Genomes Finished"
[1] "Biaka-Py.HGDP Finished"
[1] "Bidayuh.Reich2011 Finished"
[1] "Brahui.HGDP Finished"
[1] "British.1000.Genomes Finished"
[1] "Bulgarian.Hellenthal2014 Finished"
[1] "Bulgarian.Yunusbayev2011 Finished"
[1] "Burmese.Chaubey2010 Finished"
[1] "Burusho.HGDP Finished"
[1] "Buryat.Rasmussen2010 Finished"
[1] "Chechen.Yunusbayev2011 Finished"
[1] "Chukchi.Rasmussen2010 Finished"
[1] "Chuvash.Behar2010 Finished"
[1] "Colombian.1000.Genomes Finished"
[1] "Cypriot.Behar2010 Finished"
[1] "Dai.1000.Genomes Finished"
[1] "Dravidian.Reich2011 Finished"
[1] "Druze.HGDP Finished"
[1] "Dyak.Reich2011 Finished"
[1] "East.Sicilian.Hellenthal2014 Finished"
[1] "Eastern.Greenlander.Rasmussen2010 Finished"
[1] "Egyptian.Behar2010 Finished"
[1] "Emirati.Hellenthal2014 Finished"
[1] "Esan.1000.Genomes Finished"
[1] "Estonian.Raghavan2013 Finished"
[1] "Ethiopian.Jew.Behar2010 Finished"
[1] "Ethiopian.Behar2010 Finished"
[1] "Euro.Utah.1000.Genomes Finished"
[1] "Evenki.Rasmussen2010 Finished"
[1] "Fijian.Reich2011 Finished"
[1] "Finnished Finish"
[1] "Finnish.1000.Genomes Finished"
[1] "French.HGDP Finished"
[1] "Gambian.1000.Genomes Finished"
[1] "Georgian.Behar2010 Finished"
[1] "Greek.Hellenthal2014 Finished"
[1] "Gujarati.1000.Genomes Finished"
[1] "Gujarati.HapMap Finished"
[1] "Han.Beijing.1000.Genomes Finished"
[1] "Han.Dallas.HapMap Finished"
[1] "Han.South.China.1000.Genomes Finished"
[1] "Han.HGDP Finished"
[1] "Hazara.HGDP Finished"
[1] "Hungarian.Behar2010 Finished"
[1] "Iranian.Behar2010 Finished"
[1] "Iraqi.Jewish.Behar2010 Finished"
[1] "Calculating Distance To Tipperary..."
[1] "Not Far Enough."
[1] "Irish.UCD Finished"
[1] "Japanese.1000.Genomes Finished"
[1] "Jehai.Reich2011 Finished"
[1] "Kalash.HGDP Finished"
[1] "Karitiana.HGDP Finished"
[1] "Kazakh.Raghavan2013 Finished"
[1] "Khaskassian.Fedorova2013 Finished"
[1] "Khmer.HGDP Finished"
[1] "Kinh.1000.Genomes Finished"
[1] "Kumyk.Yunusbayev2011 Finished"
[1] "Kyrgyz.Raghavan2013 Finished"
[1] "Lahu.HGDP Finished"
[1] "Lezgi.Behar2010 Finished"
[1] "Lithuanian.Behar2010 Finished"
[1] "Luhya.1000.Genomes Finished"
[1] "Maasai.HapMap Finished"
[1] "Makrani.HGDP Finished"
[1] "Mamanwa.Reich2011 Finished"
[1] "Mandenka.HGDP Finished"
[1] "Manobo.Reich2011 Finished"
[1] "Mari.Raghavan2013 Finished"
[1] "Maya.HGDP Finished"
[1] "Mbuti-Py.HGDP Finished"
[1] "Melanesian.HGDP Finished"
[1] "Mende.1000.Genomes Finished"
[1] "Mexican.1000.Genomes Finished"
[1] "Miaozu.HGDP Finished"
[1] "Mongolian.HGDP Finished"
[1] "Mordovin.Yunusbayev2011 Finished"
[1] "Moroccan.Jewish.Behar2010 Finished"
[1] "Moroccan.Behar2010 Finished"
[1] "Mozabite.HGDP Finished"
[1] "Na-Dene.Rasmussen2010 Finished"
[1] "Nganassan.Rasmussen2010 Finished"
[1] "Nogai.Yunusbayev2011 Finished"
[1] "North.Italian.HGDP Finished"
[1] "Norwegian.Hellenthal2014 Finished"
[1] "Orcadian.HGDP Finished"
[1] "Oroqen.HGDP Finished"
[1] "Ossetian.Yunusbayev2011 Finished"
[1] "PNG.Southern.Highlands.Reich2011 Finished"
[1] "Palestinian.HGDP Finished"
[1] "Papuan.HGDP Finished"
[1] "Pathan.HGDP Finished"
[1] "Peruvian.1000.Genomes Finished"
[1] "Pima.HGDP Finished"
[1] "Polish.Hellenthal2014 Finished"
[1] "Polynesian.Reich2011 Finished"
[1] "Puerto.Rican.1000.Genomes Finished"
[1] "Punjabi.1000.Genomes Finished"
[1] "Romanian.Behar2010 Finished"
[1] "Russian.HGDP Finished"
[1] "San.Khomani.Hellenthal2014 Finished"
[1] "Sandawe.Hellenthal2014 Finished"
[1] "Sardinian.HGDP Finished"
[1] "Saudi.Behar2010 Finished"
[1] "Selkup.Rasmussen2010 Finished"
[1] "Sephardic.Behar2010 Finished"
[1] "She.HGDP Finished"
[1] "Sindhi.HGDP Finished"
[1] "South.Italian.Hellenthal2014 Finished"
[1] "Spanish.1000.Genomes Finished"
[1] "Surui.HGDP Finished"
[1] "Syrian.Behar2010 Finished"
[1] "Tamil.1000.Genomes Finished"
[1] "Telugu.1000.Genomes Finished"
[1] "Temuan.Reich2011 Finished"
[1] "Tibetan.Wuren2014 Finished"
[1] "Tu.HGDP Finished"
[1] "Tujia.HGDP Finished"
[1] "Tunisian.Hellenthal2014 Finished"
[1] "Turkish.Behar2010 Finished"
[1] "Turkmen.Yunusbayev2011 Finished"
[1] "Tuscan.1000.Genomes Finished"
[1] "Tuvan.Rasmussen2010 Finished"
[1] "Ukrainian.Yunusbayev2011 Finished"
[1] "Uygur.HGDP Finished"
[1] "Uzbek.Behar2010 Finished"
[1] "West.Sicilian.Hellenthal2014 Finished"
[1] "Western.Greenlander.Rasmussen2010 Finished"
[1] "Yakut.HGDP Finished"
[1] "Yemeni.Jewish.Behar2010 Finished"
[1] "Yemeni.Behar2010 Finished"
[1] "Yizu.HGDP Finished"
[1] "Yoruba.1000.Genomes Finished"
[1] "tPED files used:"
[1] "/usr/local/lib/R/site-library/AncestryMapper/extdata/Demo.tped"
[1] "1000 common SNPs found between all submitted tPED files."
[1] "1000 common SNPs found between All00 reference and all submitted tPED files"
[1] "/usr/local/lib/R/site-library/AncestryMapper/extdata/Demo.tped"
[1] "***** Number of SNPs Used: 1000"
[1] "Wrote out AMid file to, /work/tmp/AMidExample_ref143_inds567_SNPs1000.amid"

AncestryMapper documentation built on May 2, 2019, 4:29 a.m.