Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool

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Documentation for package ‘rMVP’ version 1.0.8

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MVP MVP, Memory-efficient, Visualization-enhanced, Parallel-accelerated
MVP.BRENT.Vg.Ve MVP.BRENT.Vg.Ve variance component estimation using the BRENT method
MVP.calk Calculate Kinship matrix by Blocking strategy
MVP.Data MVP.Data: To prepare data for MVP package Author: Xiaolei Liu, Lilin Yin and Haohao Zhang Build date: Aug 30, 2016 Last update: Sep 12, 2018
MVP.Data.Bfile2MVP MVP.Data.Bfile2MVP: To transform plink binary data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018
MVP.Data.Hapmap2MVP MVP.Data.Hapmap2MVP: To transform Hapmap data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018
MVP.Data.impute MVP.Data.impute: To impute the missing genotype Author: Haohao Zhang Build date: Sep 12, 2018
MVP.Data.Kin Kinship
MVP.Data.Map MVP.Data.Map: To check map file Author: Haohao Zhang Build date: Sep 12, 2018
MVP.Data.MVP2Bfile MVP.Data.MVP2Bfile: To transform MVP data to binary format Author: Haohao Zhang Build date: Sep 12, 2018
MVP.Data.Numeric2MVP MVP.Data.Numeric2MVP: To transform Numeric data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018
MVP.Data.PC Principal component analysis
MVP.Data.Pheno MVP.Data.Pheno: To clean up phenotype file Author: Haohao Zhang Build date: Sep 12, 2018
MVP.Data.VCF2MVP MVP.Data.VCF2MVP: To transform vcf data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018
MVP.EMMA.Vg.Ve Estimate variance components using EMMA
MVP.FarmCPU Perform GWAS using FarmCPU method
MVP.FaSTLMM.LL Evaluation of the maximum likelihood using FaST-LMM method
MVP.GLM To perform GWAS with GLM and MLM model and get the P value of SNPs
MVP.HE.Vg.Ve To estimate variance component using HE regression
MVP.Hist Phenotype distribution histogram
MVP.K.VanRaden Calculate Kinship matrix by VanRaden method
MVP.MLM To perform GWAS with GLM and MLM model and get the P value of SNPs
MVP.PCA Principal Component Analysis
MVP.PCAplot PCA Plot
MVP.Report MVP.Report
MVP.Report.Density SNP Density
MVP.Report.QQplot QQ Plot
MVP.Version Print MVP Banner
pig60K Genotyped by pig 60k chip