calculateAMidsArith: Calculate genetic distances.

In AncestryMapper: Assigning Ancestry Based on Population References

Description

Calculates genetic distance between samples and population references.

Usage

calculateAMidsArith(pathTotpeds, pathToAriMedoids, AMmcapply = F, nrcores,
  seqchip = "", noseqdat = F, wd, NameOut = NULL, pathAll00)

Arguments

pathTotpeds	Character vector giving path to folder containing the plink tPED file(s) to be used.
pathToAriMedoids	Character vector giving path to folder containing the arithmetic references to be used.
AMmcapply	Logical value (TRUE or FALSE), specifying if the multicore funcion mcapply, should be used. Inappropriate for most HPC cluster systems. Default = FALSE
nrcores	Numeric value detailing how many cores should be used if AMmcapply==TRUE. If left unspecificed the number of cores will be detected and nrcores will be set to that number -2.
seqchip	Character vector specifying if only references from one main SNP chip panel are to be used. All references are marked with what chip panel they use at the end of their file names, eg 'Yoruba.HGDP.20000.Illumina.ods' May be important if your data has few SNPs in common with one panel. All toy references prepared use 'Illumina' panels. Whole Genome sequence data is specified with 'WG'. Supports custom designations, but will trigger a warning when used.
noseqdat	Logical value (TRUE or FALSE), specifying if sequence data is to be excluded, will use only references that do not have names ending in '.WG.ods/rds/rda'. Default = FALSE
wd	Character vector giving the desired working directory to house the outputs of calculateAMidsArith. If left unspecified will use current working directory.
NameOut	Character vector giving the desired prefix name for the AMid file. Default is NULL.
pathAll00	Character vector giving the path to a file containing the full data table of each dbSNP and both alleles. An example version covering the SNPs used in the example data is included. A full version can be found at: http://bit.ly/1OUstDP

Examples

## Not run: 
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.Behar2010 Finished"
[1] "Ethiopian.Jew.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.HGDP Finished"
[1] "Han.Beijing.1000.Genomes Finished"
[1] "Han.Dallas.HapMap Finished"
[1] "Han.South.China.1000.Genomes 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.Behar2010 Finished"
[1] "Moroccan.Jewish.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] "Palestinian.HGDP Finished"
[1] "Papuan.HGDP Finished"
[1] "Pathan.HGDP Finished"
[1] "Peruvian.1000.Genomes Finished"
[1] "Pima.HGDP Finished"
[1] "PNG.Southern.Highlands.Reich2011 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.Behar2010 Finished"
[1] "Yemeni.Jewish.Behar2010 Finished"
[1] "Yizu.HGDP Finished"
[1] "Yoruba.1000.Genomes Finished"
[1] "tPED files used:"
[1] "/usr/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/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.