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

## Documentation for package ‘rMVP’ version 1.0.6

- DESCRIPTION file.

## Help Pages

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