Github: https://github.com/xiaolei-lab/rMVP
Gitee(quick access in China): https://gitee.com/xiaolei-lab/rMVP

Design and Maintenance: Lilin Yin#, Haohao Zhang#, Shuhong Zhao, Xinyun Li, and Xiaolei Liu.
Contributors: Zhenshuang Tang, Jingya Xu, Dong Yin, Zhiwu Zhang, Xiaohui Yuan, Mengjin Zhu
Citation: Yin L, Zhang H, Tang Z, Xu J, Yin D, Zhang Z, Yuan X, Zhu M, Zhao S, Li X. rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated tool for Genome-Wide Association Study, Genomics, Proteomics & Bioinformatics , 2021, 19 (4), 619-628, doi: 10.1016/j.gpb.2020.10.007.

Questions, suggestions, and bug reports are welcome and appreciated: [email protected]

• Installation
• Data Preparation
  • Phenotype
  • Genotype
    • PLINK binary
    • VCF
    • Hapmap
    • Numeric
  • Genomic relationship matrix (Optional)
  • Principal Components (Optional)
• Data Input
  • Basic
  • Advanced
• Start GWAS
• Output
  • Phenotype distribution
  • SNP-density plot
  • PCA plot
  • Manhattan plot in Circular fashion
  • Manhattan plot in Rectangular fashion for single trait or method
    • Manhattan plot in Rectangular fashion for multiple traits or methods
    • Q-Q plot for single trait or method
    • Q-Q plot for multiple traits or methods
• Citation
• FAQ and Hints

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WE STRONGLY RECOMMEND TO link MKL or OpenBLAS with R to accelerate parallel computing. To install rMVP in R:

• The stable version:

install.packages("rMVP")

• The latest version:

devtools::install_github("xiaolei-lab/rMVP")

After installed successfully, rMVP can be loaded by typing

library(rMVP)

Typing ?rMVP could get the details of all parameters.

For more help on Windows installation, see the wiki page (Chinese)

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We suggest to provide the phenotype file, because users needn't to manually pre-treat the order of phenotype and genotype individuals, rMVP could automatically adjust the order of phenotype file to be consistent with genotype file. Note that if the phenotype is provided in data conversion, rMVP will generate a new phenotype file, please remember to load it for analysis rather than original one.

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If you have genotype data in PLINK Binary format (details see http://zzz.bwh.harvard.edu/plink/data.shtml#bed):  

fileBed, name of genotype data in PLINK Binary format
fileKin, TRUE or FALSE, if TRUE, kinship matrix represents relationship among individuals will be calculated
filePC, TRUE or FALSE, if TRUE, principal component analysis will be performed
out, prefix of output file
maxLine, number, the number of markers read into memory

# Full-featured function (Recommended)
MVP.Data(fileBed="plink",
         filePhe=NULL,
         fileKin=FALSE,
         filePC=FALSE,       
         #maxLine=10000,
         out="mvp.plink"
         )
         
# Only convert genotypes
MVP.Data.Bfile2MVP(bfile="plink", out='mvp', maxLine=1e4) # the genotype data should be fully imputed before using this function

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If you have genotype data in VCF format:
fileVCF, name of genotype data in VCF format
filePhe, name of phenotype data
sep.phe, separator of phenotype file
fileKin, TRUE or FALSE, if TRUE, kinship matrix represents relationship among individuals will be calculated
filePC, TRUE or FALSE, if TRUE, principal component analysis will be performed
out, the prefix of output file

##fileformat=VCFv4.2
##fileDate=20171105
##source=PLINKv1.90
##contig=<ID=1,length=2>
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	-9_CZTB0004	-9_CZTB0006	-9_CZTB0008	-9_CZTB0010	-9_CZTB0011	-9_CZTB0012
1	1	10000235	A	C	.	.	PR	GT	0/1	0/0	0/0	0/0	0/0	0/1
1	1	10000345	A	G	.	.	PR	GT	0/0	0/0	0/0	0/0	1/1	1/1
1	1	10004575	G	.	.	.	PR	GT	0/0	0/0	0/0	0/0	0/0	0/0
1	1	10006974	C	T	.	.	PR	GT	0/0	0/0	0/1	1/1	0/1	1/1
1	1	10006986	A	G	.	.	PR	GT	0/0	0/0	0/1	./.	1/1	1/1

# Full-featured function (Recommended)
MVP.Data(fileVCF="myVCF.vcf",
         #filePhe="Phenotype.txt",
         fileKin=FALSE,
         filePC=FALSE,
         out="mvp.vcf"
         )

# Only convert genotypes
MVP.Data.VCF2MVP("myVCF.vcf", out='mvp') # the genotype data should be fully imputed before using this function

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If you have genotype data in Hapmap format:

fileHMP, a string or a string vector, e.g. fileHMP = "hapmap.txt" or fileHMP = c("chr1.hmp.txt", "chr2.hmp.txt", "chr3.hmp.txt")
filePhe, name of phenotype file
sep.phe, separator of phenotype file
fileKin, TRUE or FALSE, if TRUE, kinship matrix represents relationship among individuals will be calculated
filePC, TRUE or FALSE, if TRUE, principal component analysis will be performed
out, the prefix of output file
maxLine, number, the number of markers read into memory

hapmap.txt

# Full-featured function (Recommended)
MVP.Data(fileHMP="hapmap.txt",
         filePhe="Phenotype.txt",
         sep.hmp="\t",
         sep.phe="\t",
         SNP.effect="Add",
         fileKin=FALSE,
         filePC=FALSE,
         #maxLine=10000,
         out="mvp.hmp"
         )

# Only convert genotypes
MVP.Data.Hapmap2MVP("hapmap.txt", out='mvp') # the genotype data should be fully imputed before using this function

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If you have genotype data in Numeric (m * n, m rows and n columns, m is the number of SNPs, n is the number of individuals) format:  

fileNum, name of genotype data in Numeric format
filePhe, name of phenotype file
fileMap, name of map file, a header should be added, e.g. SNP Chr Pos
sep.num, separator of Numeric file
sep.phe, separator of phenotype file
type.geno, the type of data in Numeric file, "char", "integer", or "double"
fileKin, TRUE or FALSE, if TRUE, kinship matrix represents relationship among individuals will be calculated
filePC, TRUE or FALSE, if TRUE, principal component analysis will be performed
out, the prefix of output file
maxLine, number, the number of markers read into memory
auto_transpose, bool, if auto_transpose = TRUE, it is automatically transposed to ensure that the number of rows (markers) is greater than the number of columns (individuals).

# Full-featured function (Recommended)
MVP.Data(fileNum="Numeric.txt",
         filePhe="Phenotype.txt",
         fileMap="Map.txt",
         sep.num="\t",
         sep.map="\t", 
         sep.phe="\t",
         fileKin=FALSE,
         filePC=FALSE,
         #maxLine=10000,
         out="mvp.num"
         )

# Only convert genotypes
MVP.Data.Numeric2MVP("Numeric.txt", out='mvp', maxLine=1e4, auto_transpose=T) # the genotype data should be fully imputed before using this function

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If you have Kinship matrix data that represents the relationship among individuals

fileKin, name of Kinship matrix data, the dimension is n * n (n is sample size), no taxa names included
sep.kin, separator of Kinship file

mvp.kin.txt

# read from file
MVP.Data.Kin("mvp.kin.txt", out="mvp", maxLine=1e4, sep='\t')

# calculate from mvp_geno_file
MVP.Data.Kin(TRUE, mvp_prefix='mvp.vcf', out='mvp')

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If you have Principal Components data

filePC, name of Principal Components matrix data, the dimension is n * nPC (n is sample size, nPC is number of first columns of PCs), no taxa names and header row included
sep.pc, separator of Principal Components file

mvp.pc.txt

# read from file
MVP.Data.PC("mvp.pc.txt", out='mvp', sep='\t')

# calculate from mvp_geno_file
MVP.Data.PC(TRUE, mvp_prefix='mvp.vcf', pcs.keep=5)

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At least you should prepare three datasets: genotype, phenotype, and map

genotype, genotype data generated by 'MVP.Data' function
phenotype, phenotype data, the first column is taxa name and second column is phenotype value. Note that if the phenotype is provided in data conversion, rMVP will generate a new phenotype file, please remember to load it for analysis rather than original one
map, SNP map information, the first column is SNP name, the second column is Chromosome ID, the third column is phsical position

genotype <- attach.big.matrix("mvp.geno.desc")
phenotype <- read.table("mvp.phe",head=TRUE)
map <- read.table("mvp.geno.map" , head = TRUE)

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You can load the prepared Kinship matrix and Covariates data generated by 'MVP.Data' function
Kinship, Kinship matrix, the dimension of Kinship matrix is n * n (n is sample size), no taxa names included
Covariates, Covariates matrix, the dimension of Covariates matrix is n * nCV (n is sample size, nCV is number of covariates, no taxa names and header row included
NOTE: If pcs have been added in covariate files, PLEASE DO NOT assign value to nPC.GLM, nPC.MLM, nPC.FarmCPU.

```r
Kinship <- attach.big.matrix("mvp.kin.desc")
Covariates_PC <- bigmemory::as.matrix(attach.big.matrix("mvp.pc.desc"))

If you have additional environmental fixed effects (e.g., breed, sex) or covariates (weight), please use it as following:

Covariates <- model.matrix.lm(~as.factor(breed)+as.factor(sex)+as.numeric(weight), data=yourdata, na.action = "na.pass")
# NA is acceptable in 'Covariates'

# if you are supposed to take PC to covariate
Covariates <- cbind(Covariates, Covariates_PC)

NOTE: rMVP has no function of adjusting the order of individuals in covariates. PLEASE make sure the order of individuals in covariates file must be consistent with that in genotype file.

If you have prepared Kinship matrix and Covariates data generated by other software packages, see Kinship and Principal Components

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Three models are included in MVP package: General Linear Model (GLM), Mixed Linear Model (MLM), and FarmCPU.

phe, phenotype data
geno, genotype data
map, map data
K, Kinship matrix
CV.GLM, Covariates added in GLM
CV.MLM, Covariates added in MLM
CV.FarmCPU, Covariates added in FarmCPU
If you don't want to add PCs as covariates, please comment out the parameters instead of setting the nPC to 0
please attention that if nPC.GLM > 0, no PCs should be added in CV.GLM
nPC.GLM, number of first columns of Principal Components added in GLM
please attention that if nPC.MLM > 0, no PCs should be added in CV.MLM
nPC.MLM, number of first columns of Principal Components added in MLM
please attention that if nPC.FarmCPU > 0, no PCs should be added in CV.FarmCPU
nPC.FarmCPU, number of first columns of Principal Components added in FarmCPU
maxLine, the number of markers handled at a time, smaller value would reduce the memory cost
ncpus, number of CPUs used for parallel computation, If not set, all CPUs will be used by default
vc.method, methods of variance components analysis, three methods are avaiblable, "BRENT", "EMMA", and "HE"
maxLoop, a parameter for FarmCPU only, the maximum iterations allowed in FarmCPU
method.bin, a parameter for FarmCPU only, two options are available: 'static' or 'FaST-LMM'
permutation.threshold, if TRUE, a threshold of permutation will be used in manhattan plot. The phenotypes are permuted to break the relationship with the genotypes. The experiment is replicated for a number of times. A vector of minimum p value of all experiments is recorded and the 95% quantile value of this vector is recommended to be used as significant threshold
permutation.rep, number of permutation replicates, only used when permutation.threshold is TRUE
threshold, 0.05/marker size, a cutoff line on manhattan plot
method, models for association tests, three models are available in MVP, "GLM", "MLM", and "FarmCPU", one or two or three models can be selected for association tests
file.output, a Boolean value or a string vector. If TRUE, output all types of files. If FALSE, no files are output. For string vectors, the available values are c("pmap", "pmap.signal", "plot", "log"). Among them, pmap represents all SNP P-Val files, pmap.signal represents significant SNP files, Plot represents visualization results, and log represents log files.

imMVP <- MVP(
    phe=phenotype,          #NA is acceptable in phenotype
    geno=genotype,
    map=map,
    #K=Kinship,             #if you have pre-computed GRM, please keep there open, otherwise rMVP will compute it automatically
    #CV.GLM=Covariates,     #if you have environmental covariates, please keep all 'CV.*' open
    #CV.MLM=Covariates,
    #CV.FarmCPU=Covariates,
    nPC.GLM=5,              #if you have added PCs into covariates, please keep there closed
    nPC.MLM=3,              #if you don't want to add PCs as covariates, please comment out the parameter instead of setting it to 0.
    nPC.FarmCPU=3,
    maxLine=10000,          #smaller value would reduce the memory cost
    #ncpus=10,
    vc.method="BRENT",      #only works for MLM
    method.bin="static",    # "FaST-LMM", "static" (#only works for FarmCPU)
    threshold=0.05,
    method=c("GLM", "MLM", "FarmCPU"),
    file.output=c("pmap", "pmap.signal", "plot", "log")
)

If you have more than one phenotype

for(i in 2:ncol(phenotype)){
  imMVP <- MVP(
    phe=phenotype[, c(1, i)],
    geno=genotype,
    map=map,
    #K=Kinship,
    #CV.GLM=Covariates,
    #CV.MLM=Covariates,
    #CV.FarmCPU=Covariates,
    nPC.GLM=5,
    nPC.MLM=3,
    nPC.FarmCPU=3,
    maxLine=10000,
    #ncpus=10,
    vc.method="BRENT",
    method.bin="static",
    threshold=0.05,
    method=c("GLM", "MLM", "FarmCPU"),
    file.output=c("pmap", "pmap.signal", "plot", "log")
  )
  gc()
}

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MVP automatically outputs high-quality figures, three types of figure formats are available (".jpg",".pdf",".tiff", default is ".jpg"). Users could also adjust the output figure using about 50 parameters in MVP.Report(). MVP.Report() not only accept the final return of MVP(), but also accepts results from third-party software packages, such as PLINK, GEMMA, GAPIT, TASSEL, and FarmCPU. The result from third-party software packages should at least contain four columns, which are marker name, chromosome, physical position, and P-value of a trait, results of more than one trait could be sequentially appended column by column. Typing ?MVP.Report() to see details of all parameters and typing data(pig60K) or data(cattle50K) to load demo datasets. Type ?MVP.Repory to see parameter details.

> data(pig60K)   #GWAS result of MLM
> data(cattle50K)   #SNP effects calculated from rrblup

> head(pig60K)

          SNP Chromosome Position    trait1     trait2     trait3
1 ALGA0000009          1    52297 0.7738187 0.51194318 0.51194318
2 ALGA0000014          1    79763 0.7738187 0.51194318 0.51194318
3 ALGA0000021          1   209568 0.7583016 0.98405289 0.98405289
4 ALGA0000022          1   292758 0.7200305 0.48887140 0.48887140
5 ALGA0000046          1   747831 0.9736840 0.22096836 0.22096836
6 ALGA0000047          1   761957 0.9174565 0.05753712 0.05753712

> head(cattle50K)

   SNP chr    pos Somatic cell score  Milk yield Fat percentage
1 SNP1   1  59082        0.000244361 0.000484255    0.001379210
2 SNP2   1 118164        0.000532272 0.000039800    0.000598951
3 SNP3   1 177246        0.001633058 0.000311645    0.000279427
4 SNP4   1 236328        0.001412865 0.000909370    0.001040161
5 SNP5   1 295410        0.000090700 0.002202973    0.000351394
6 SNP6   1 354493        0.000110681 0.000342628    0.000105792

In the demo datasets, the first three columns are marker name, chromosome, and physical position, respectively, the rest columns are the P-value or effect of multiple traits. Number of traits is theoretically unlimited.

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phe, phenotype data
file.type, format of output figure
breakNum, number of breaking points for phenotype when plotting distribution
dpi, resolution of output figure

MVP.Hist(phe=phenotype, file.type="jpg", breakNum=18, dpi=300)

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plot.type, four options ("d", "c", "m", "q"); if "d", draw SNP-density plot
bin.size, the window size for counting SNP number
bin.max, maximum SNP number, for windows, which has more SNPs than bin.max, will be painted in same color
col, colors for separating windows with different SNP density
file.type, format of output figure
dpi, resolution of output figure

MVP.Report(pig60K[, c(1:3)], plot.type="d", col=c("darkgreen", "yellow", "red"), file.type="jpg", dpi=300)

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pca, the first three columns of principle components
Ncluster, cluster number
class, the class of all individuals, for example: "breed", "location"...
col, colors for each cluster
pch, point shape for each cluster
file.type, format of output figure
dpi, resolution of output figure

pca <- attach.big.matrix("mvp.pc.desc")[, 1:3]
#pca <- prcomp(t(as.matrix(genotype)))$x[, 1:3]
MVP.PCAplot(PCA=pca, Ncluster=3, class=NULL, col=c("red", "green", "yellow"), file.type="jpg")

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For GWAS results:

> MVP.Report(pig60K,plot.type="c",chr.labels=paste("Chr",c(1:18,"X"),sep=""),r=0.4,cir.legend=TRUE,
        outward=FALSE,cir.legend.col="black",cir.chr.h=1.3,chr.den.col="black",file.type="jpg",
        memo="",dpi=300)

> MVP.Report(pig60K,plot.type="c",r=0.4,col=c("grey30","grey60"),chr.labels=paste("Chr",c(1:18,"X"),sep=""),
      threshold=c(1e-6,1e-4),cir.chr.h=1.5,amplify=TRUE,threshold.lty=c(1,2),threshold.col=c("red",
      "blue"),signal.line=1,signal.col=c("red","green"),chr.den.col=c("darkgreen","yellow","red"),
      bin.size=1e6,outward=FALSE,file.type="jpg",memo="",dpi=300)

#Note:
1. if signal.line=NULL, the lines that crosse circles won't be added.
2. if the length of parameter 'chr.den.col' is not equal to 1, SNP density that counts 
   the number of SNP within given size('bin.size') will be plotted around the circle.

For GS/GP results:

> MVP.Report(cattle50K,plot.type="c",LOG10=FALSE,outward=TRUE,matrix(c("#4DAF4A",NA,NA,"dodgerblue4",
            "deepskyblue",NA,"dodgerblue1", "olivedrab3", "darkgoldenrod1"), nrow=3, byrow=TRUE),
            chr.labels=paste("Chr",c(1:29),sep=""),threshold=NULL,r=1.2,cir.chr.h=1.5,cir.legend.cex=0.5,
            cir.band=1,file.type="jpg", memo="",dpi=300,chr.den.col="black")
        
#Note: 
Parameter 'col' can be either vector or matrix, if a matrix, each trait can be plotted in different colors.

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For GWAS results:

> MVP.Report(pig60K,plot.type="m",LOG10=TRUE,threshold=NULL,col=c("dodgerblue4","deepskyblue"), cex=0.7,
            chr.den.col=NULL,file.type="jpg",memo="",dpi=300)

> MVP.Report(pig60K, plot.type="m", col=c("dodgerblue4","deepskyblue"), LOG10=TRUE, ylim=NULL,
        threshold=c(1e-6,1e-4), threshold.lty=c(1,2), threshold.lwd=c(1,1), threshold.col=c("black",
        "grey"), amplify=TRUE,chr.den.col=NULL, signal.col=c("red","green"), signal.cex=c(1,1),
        signal.pch=c(19,19),file.type="jpg",memo="",dpi=300)

> MVP.Report(pig60K, plot.type="m", LOG10=TRUE, ylim=NULL, threshold=c(1e-6,1e-4),threshold.lty=c(1,2),
        col=c("grey60","grey30"), threshold.lwd=c(1,1), threshold.col=c("black","grey"), amplify=TRUE,
        chr.den.col=c("darkgreen", "yellow", "red"),bin.size=1e6,signal.col=c("red","green"),
        signal.cex=c(1,1),signal.pch=c(19,19),file.type="jpg",memo="",dpi=300)
        
#Note:
if the length of parameter 'chr.den.col' is bigger than 1, SNP density that counts 
   the number of SNP within given size('bin.size') will be plotted.

For GS/GP results:

> MVP.Report(cattle50K, plot.type="m", band=0, LOG10=FALSE, ylab="Abs(SNP effect)",threshold=0.015,
        threshold.lty=2, threshold.lwd=1, threshold.col="red", amplify=TRUE, signal.col=NULL,
        col=c("dodgerblue4","deepskyblue"), chr.den.col=NULL, file.type="jpg",memo="",dpi=300)

#Note: 
if signal.col=NULL, the significant SNPs will be plotted with original colors.

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> MVP.Report(pig60K, plot.type="m", multracks=TRUE, threshold=c(1e-6,1e-4),threshold.lty=c(1,2), 
        threshold.lwd=c(1,1), threshold.col=c("black","grey"), amplify=TRUE,bin.size=1e6,
        chr.den.col=c("darkgreen", "yellow", "red"), signal.col=c("red","green"),signal.cex=c(1,1),
        file.type="jpg",memo="",dpi=300)

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> MVP.Report(pig60K,plot.type="q",conf.int.col=NULL,box=TRUE,file.type="jpg",memo="",dpi=300)

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> MVP.Report(imMVP,plot.type="q",col=c("dodgerblue1", "olivedrab3", "darkgoldenrod1"),threshold=1e6,
        signal.pch=19,signal.cex=1.5,signal.col="red",conf.int.col="grey",box=FALSE,multracks=
        TRUE,file.type="jpg",memo="",dpi=300)

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For MVP (Please cite MVP package for all the functions):
Yin L, Zhang H, Tang Z, Xu J, Yin D, Zhang Z, Yuan X, Zhu M, Zhao S, Li X. rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated tool for Genome-Wide Association Study, Genomics, Proteomics & Bioinformatics, 2021, 19 (4), 619-628, doi: 10.1016/j.gpb.2020.10.007.

For calculation of K matrix:
Vanraden, P. M. "Efficient Methods to Compute Genomic Predictions." Journal of Dairy Science 91.11(2008):4414-4423.

For GLM(PC) model:
Price, Alkes L., et al. "Principal components analysis corrects for stratification in genome-wide association studies." Nature genetics 38.8 (2006): 904.

For MLM(K) model:
Yu, Jianming, et al. "A unified mixed-model method for association mapping that accounts for multiple levels of relatedness." Nature genetics 38.2 (2006): 203.

For MLM(PCA+K) model:
Price, Alkes L., et al. "Principal components analysis corrects for stratification in genome-wide association studies." Nature genetics 38.8 (2006): 904.

For FarmCPU model:
Liu, Xiaolei, et al. "Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies." PLoS genetics 12.2 (2016): e1005767.

For variance components:
> HE: Zhou, Xiang. "A unified framework for variance component estimation with summary statistics in genome-wide association studies." The annals of applied statistics 11.4 (2017): 2027.
> EMMA/P3D:
1. Kang, Hyun Min, et al. "Efficient control of population structure in model organism association mapping." Genetics 178.3 (2008): 1709-1723.
2. Zhang, Zhiwu, et al. "Mixed linear model approach adapted for genome-wide association studies." Nature genetics 42.4 (2010): 355.
> Fast-lmm: Lippert, Christoph, et al. "FaST linear mixed models for genome-wide association studies." Nature methods 8.10 (2011): 833.

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🆘 Question1: Failing to install "devtools":

ERROR: configuration failed for package ‘git2r’

removing ‘/Users/acer/R/3.4/library/git2r’

ERROR: dependency ‘git2r’ is not available for package ‘devtools’

removing ‘/Users/acer/R/3.4/library/devtools’

😋 Answer: Please try following codes in terminal:

apt-get install libssl-dev/unstable

🆘 Question2: When installing packages from Github with "devtools", an error occurred:

Error in curl::curl_fetch_disk(url, x$path, handle = handle): Problem with the SSL CA cert (path? access rights?)

😋 Answer: Please try following codes and then try agian.

library(httr)
set_config(config(ssl_verifypeer = 0L))

🆘 Question3: When installing MVP:

Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress, : write failed ERROR: lazy loading failed for package ‘MVP’ removing ‘/home/liuxl/R/x86_64-pc-linux-gnu-library/3.3/MVP’ Warning message: In install.packages("MVP_1.0.1.tar.gz", repos = NULL) : installation of package ‘MVP_1.0.1.tar.gz’ had non-zero exit status

😋 Answer: It is probably an issue caused by disk full, please check disk space.

Questions, suggestions, and bug reports are welcome and appreciated. ➡️

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