2011-10-22

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R HWE LD SNP plink GWAViewer

こちらの講義に出席してみる
RのGenetics関係のパッケージのページ(こちら)
RでHWE

library(HardyWeinberg)
x <- c(100, 50, 10)
HW.test <- HWChisq(x, verbose = TRUE)

HW.lrtest <- HWLratio(x, verbose = TRUE)

HW.exacttest <- HWExact(x, verbose = TRUE)

> library(HardyWeinberg)
> x <- c(100, 50, 10)
> HW.test <- HWChisq(x, verbose = TRUE)
Chi-square test with continuity correction for Hardy-Weinberg equilibrium
Chi2 =  0.799458 p-value =  0.3712555 D =  -2.34375 
> 
> HW.lrtest <- HWLratio(x, verbose = TRUE)
G2 = 1.123345 p-value = 0.2891993 
> 
> HW.exacttest <- HWExact(x, verbose = TRUE)
Haldane's Exact test for Hardy-Weinberg equilibrium
sample counts: nAA =  100 nAB =  50 nBB =  10 
H0: HWE (D==0), H1: D <> 0 
D =  -2.34375 p =  0.3671761 
>

# make random compositions that are in HWE

set.seed(123)

m <- 100 # number of markers
n <- 100 # sample size

out <- HWData(n,m)
Xc <- out$Xc
out <- HWTernaryPlot(Xc,100,region=1,vertex.cex=2,signifcolour=TRUE)

library(mapLD)
data(SNPdata)
getLD <- mapLD(SNPdata = SNPdata,
locusID.col = 'markerID',
subjectID.col = 'subjectID',
allele.cols = 1:2,
WhichGene = NA,
outgraph = NA)

plinkの出力ファイル一覧(こちら)

Filename	Main associated command(s)	Description
plink.adjust	 --adjust	 Adjusted significance values (multiple testing)
plink.assoc	 --assoc	 Association results
plink.assoc.hap	 --hap-assoc	 Haplotype-based association results
plink.assoc.linear	 --linear	 Linear regression model
plink.assoc.logistic	 --logistic	 Logistic regression model
plink.assoc.mperm	 --assoc --mperm	 maxT permutation empirical p-values
plink.assoc.perm	 --assoc --perm	 Adaptive permutation empirical p-values
plink.assoc.proxy	 --proxy-assoc	 Proxy association results
plink.assoc.set	 --assoc --set	 Set-based association results
plink.bed	 --make-bed	 Binary PED file
plink.bim	 --make-bed	 Binary MAP file
plink.chap	 --chap	 Conditional haplotype tests
plink.cov	 --write-covar	 Ordered, filtered covariate file
plink.clumped	 --clump	 LD-based results clumping
plink.clumped.best	 --clump-best	 Single best LD-based clumping
plink.clumped.ranges	 --clump-range	 Gene/region report for clumps
plink.cluster0	 --cluster	 Progress of IBS clustering
plink.cluster1	 --cluster	 IBS cluster solution, format 1
plink.cluster2	 --cluster	 IBS cluster solution, format 2
plink.cluster3	 --cluster	 IBS cluster solution, format 3
plink.cluster3.missing	 --cluster-missing	 IBM cluster solution, format 3
plink.cmh	 --mh	 Cochran-Mantel-Haenszel test 1
plink.cmh2	 --mh2	 Cochran-Mantel-Haenszel test 2
plink.cnv.indiv	 --cnv-list	 Copy number variant per individual summary
plink.cnv.overlap	 --cnv-list	 Copy number variant overlap
plink.cnv.summary	 --cnv-list	 Copy number variant summary
plink.cnv.summary.mperm	 --cnv-list	 Copy number variant test
plink.diff	 --merge-mode 6/7	 Difference file
plink.epi-cc1	 --epistasis	 Epistasis: case/control pairwise results
plink.epi-cc2	 --epistasis	 Epistasis: case/control summary results
plink.epi-co1	 --epistasis --case-only	 Epistasis: case-only pairwise results
plink.epi-co2	 --epistasis --case-only	 Epistasis: case-only summary results
plink.fam	 --make-bed	 Binary FAM file
plink.fmendel	 --mendel	 Mendel errors, per family
plink.frq	 --freq	 Allele frequency table
plink.frq.count	 --freq --counts	 Allele counts table
plink.frq.hap	 --hap-freq	 Allele frequency table
plink.genepi.dat	 --genepi	 Gene-based epistasis R dataset
plink.genepi.R	 --genepi	 Gene-based epistasis R script
plink.genome	 --genome	 Genome-wide IBD/IBS pairwise measures
plink.het	 --het	 Individual inbreeding coefficients
plink.hh		 List of heterozygous haploid genotypes (SNPs/individuals)
plink.hom	 --homozyg-snp --homozyg-kb	 Runs of homozygosity
plink.hom.overlap	 --homozyg-group	 Pools of overlapping runs of homozygosity
plink.homog	 --homog	 Between strata homogeneity test
plink.hwe	 --hardy	 Hardy-Weinberg test statistics
plink.imendel	 --mendel	 Mendel errors, per individual
plink.imiss	 --missing	 Missing rates, per individual
plink.info	 --recodeHV	 Info file for Haploview filesets
plink.irem	 --mind	 List of individuals removed for low genotyping
plink.imputed.map	 --hap-impute	 Imputed from multi-marker predictors
plink.impute.ped	 --hap-impute	 Imputed from multi-marker predictors
plink.list	 --list	 Recoded LIST file
plink.lmendel	 --mendel	 Mendel errors, per locus
plink.lmiss	 --missing	 Missing rates, per locus
plink.log		 Log file (always generated)
plink.map	 --recode	 Recoded MAP file
plink.mdist	 --cluster --matrix	 IBS distance matrix
plink.mdist.missing	 --cluster-missing	 IBM distance matrix
plink.mendel	 --mendel	 Mendel errors, per error
plink.mishap	--hap	 List of SNPs that show problem phasing (could not be found or on wrong chromosome)
plink.missing	 --test-missing	 Test of differences in C/C missing rates
plink.missing.hap	 --test-mishap	 Haplotype-based test of non-random genotyping failure
plink.missnp	--merge	 List of SNPs that show strand problems when merging files (more than 2 alleles)
plink.model	 --model	 Full-model association results
plink.model.best.mperm	 --model --mperm	 Best full-model association max(T) permutation results
plink.model.best.perm	 --model --perm	 Best full-model association adaptive permutation results
plink.model.gen.mperm	 --model --mperm --model-gen	 Genotypic association max(T) permutation results
plink.model.gen.perm	 --model --perm --model-gen	 Genotypic association adaptive permutation results
plink.model.dom.mperm	 --model --mperm --model-dom	 Dominant association max(T) permutation results
plink.model.dom.perm	 --model --perm --model-dom	 Dominant association adaptive permutation results
plink.model.trend.mperm	 --model --mperm --model-trend	 Trend test association max(T) permutation results
plink.model.trend.perm	 --model --perm --model-trend	 Trend test association adaptive permutation results
plink.model.rec.mperm	 --model --mperm --model-rec	 Recessive association max(T) permutation results
plink.model.rec.perm	 --model --perm --model-rec	 Recessive association adaptive permutation results
plink.nof		 List of SNPs with no observed founders
plink.nosex		 List of individuals with ambiguous sex code
plink.nearest	--cluster --neighbour	 Nearest neighbour (IBS) statistics
plink.pdump	 --pedigree	 Information on pedigree structure
plink.ped	 --recode	 Recoded PED file
plink.phase-*	 --hap --phase	 Haplotype phases (one file per locus)
plink.plist	 --plist	 Pairwise list of two people's genotypes
plink.proxy.impute	 --proxy-impute	 Proxy imputation output
plink.proxy.impute.dosage	 --proxy-impute --proxy-dosage	 Proxy imputation dosage output
plink.proxy.report	 --proxy-assoc	 Verbose proxy association output
plink.prune.in	 --indep --indep-pairwise	 List of remaining SNPs (i.e. not pruned)
plink.prune.out	 --indep --indep-pairwise	 List of pruned-out SNPs
plink.qassoc	 --assoc	 Quantitative trait association results
plink.qassoc.gxe	 --gxe	 Quantitative trait interaction results
plink.range.report	 --cnv-verbose-report-regions	 Listing of CNVs by genes/regions
plink.raw	 --recodeAD	 Recoded additive/dominance format file
plink.snplist	 --write-snplist	 List of SNPs in the dataset
plink.T2	 --T2	 Hotelling's T(2) test results
plink.tdt	 --tdt	 TDT/parenTDT asymptotic results
plink.tdt.hap	 --tdt	 TDT/parenTDT permutaion results
plink.tdt.mperm	 --tdt	 TDT/parenTDT max(T) permutation results
plink.tdt.perm	 --tdt	 TDT/parenTDT adaptive permutation results
plink.tdt.poo	 --tdt --poo	 TDT parent-of-origin results
plink.tdt.poo.mperm	 --tdt --poo --mperm	 TDT parent-of-origin max(T) permutation results
plink.tdt.poo.perm	 --tdt --poo --perm	 TDT parent-of-origin adaptive permutation results
plink.tdt.poo.set	 --tdt --poo --set --mperm	 TDT parent-of-origin set-based results
plink.tdt.set	 --tdt --set --mperm	 TDT/parenTDT set-based results
plink.tfam	 --transpose / --tfile	 FAM for for transposed fileset
plink.tped	 --transpose / --tfile	 PED file for transposed fileset
plink.twolocus	 --twolocus	 SNP x SNP contingency table

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