rehh——An R Package

正向选择,人类遗传学,群体遗传学

rehh : An R Package吴珂皓 2012年3月29日星期四

正向选择,人类遗传学,群体遗传学

rehh An R package to detect footprints of selection in genome-wide SNPdata from haplotype structure

institut national de la recherche agronomique ,France

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the Brief Introduction of rehh An R packageTo detect the footprint of selection Based on SNP data

Using EHH(Extended Homozygosity Haplotype)Including computation: EHH(Extended Homozygosity Haplotype) iHS(within population) Rsb(across pairs of populations) ….

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About positive selection

positive selection purifying selection

balancing selection

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About EHH EHH: Extended Homozygosity HaplotypePresented firstly by Pardis C. Sabeti the probability that two randomly chosen haplotypes carrying the

candidate core haplotype are homozygous for the entire intervalspanning the core region to a given locus (Sabeti P.C et al. 2002).

Sabeti PC, et al. Detecting recent positive selection in the human genome from haplotype structure.

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About EHH12 3 4 5 6 7 8 9 1 2 3 4 5 6 7 8 9 0

A

G

C

T

12 3 4 5 6 7 8 9

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About REHHRelative EHH is the ratio of the EHH on the tested core haplotype compared with the EHH of the grouped set of core haplotypes at the region not including the core haplotype tested.

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About iHH integrated EHH (iHH) : summed over both directions away from the coreSNP

The expectation and standard deviation of ln(iHHA/iHHD) are estimated from the empirical distribution at SNPs whose derived allele frequency p matches the frequency at the core SNP.

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About EHHS EHHS: decay of EHH of an individual SNP site

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About iES

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About Rsb

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About Input File

SNP information file

SNP rs6718902 ……..

chromosome 2

base position 191838204

ancestral allele 1

derived allele 2

genotype data file

name 1 2 ……….

SNP1 1 1

SNP2 2 2

SNP3 2 1

SNP4 1 1

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About Input File

data2haplohh()CHI<-data2haplohh("CHI.hap","CHI.inp",min_maf=0,min_perc_geno.hap=100,min_perc_geno.snp=100,=NA,popsel=NA,recode.allele=FALSE)

parametero

min_maf

SNPs displaying a MAF<min_maf will be discard

o

min_perc_geno.hapmin_perc_geno.snp popsel recode.allele

Haplotypes with less than min_perc_geno.hapSNPs genotyped on less than min_perc_geno.snp

percent SNPs genotyped will be discardo

percent haplotypes will be discardo o o

name of chromosome code of population considered if true ,alleles will be recoded according to the map file

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About calculation calc_ehh()calc_ehhs()

EHH and iHH computationEHHS and iES computation

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About calculation scan_hh()encode in C 140 individuals , 1424 SNPs 3.2GHz 3.3second

scan_hh(CHI,limhaplo=2,limehh=0.05,limehhs=0.05)o o o

limhaplo limehh

minimal number of haplotypes limit below which EHH stops to be evaluated

limehhs

limit below which EHHS stops to be evaluated

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About calculation ies2rsb(hh_pop1,hh_pop2,popname1=NA,popname2=NA,method="b

ilateral")Compute Rsb ( standardized ratio of iES from two populations ) hh_pop1o

a matrix with nsnps rows and six columns – – – – – – chromosome name position frequency of ancestral alleles iHH of ancestral alleles iHH for the derived allele iES

popname1 method

name of population bilateral or unilateral

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About calculation ihh2ihs(res_ihh,freqbin=0.025,minmaf=0.05)Compute his ( standardized iHH)o

res_ihh

a matrix with nsnps rows and six columns – chromosome name – position – frequency of ancestral alleles – iHH of ancestral alleles – iHH for the derived allele – iES

o

freqbin Size of the bin to standardize log(iHH1/iHH2) according to the underlying Derived

Allele frequency. Allele frequency bins vary from minmaf to 1-minmaf per step of size freqbin. Iffreqbin is set to 0 (e.g. in the case of a large number of SNPs and few haplotypes), standardization is performed considering each observed frequency as a frequency class.o

minmaf SNPs with a MAF lower than minmaf will be discard

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About calculation distribplot(data,col=c("blue","red"),main="his distribution",xlab="iHS")

Plot the observed distribution of standarized iHS or Rsb values together with the expected standard Gaussian distribution