Type: | Package |
Title: | Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for Genome-Wide Association Study with Graphical User Interface |
Version: | 4.0.2 |
Date: | 2020-10-8 |
Author: | Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming |
Maintainer: | Yuanming Zhang<soyzhang@mail.hzau.edu.cn> |
Description: | Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes and all the nonzero effects were further identified by likelihood ratio test for true QTL. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, Wang SB, Dunwell JM, Zhang YM, Wu R (2018) <doi:10.1093/bib/bbw145>. |
Depends: | R (≥ 3.5.0),shiny,lars |
Imports: | Rcpp (≥ 0.12.14),methods,foreach,ncvreg,coin,shinyjs,data.table,doParallel,sampling,bigmemory,mrMLM,sbl |
License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
LinkingTo: | Rcpp,RcppEigen |
NeedsCompilation: | yes |
Packaged: | 2020-10-08 03:57:06 UTC; <e4><ba><9a><e9><9b><af> |
Repository: | CRAN |
Date/Publication: | 2020-10-08 10:20:02 UTC |
Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for Genome-Wide Association Study with Graphical User Interface
Description
Description: Conduct multi-locus genome-wide association study under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). First, each marker on the genome is scanned. Bonferroni correction is replaced by a less stringent selection criterion for significant test. Then, all the markers that are potentially associated with the trait are included in a multi-locus genetic model, their effects are estimated by empirical Bayes and all the nonzero effects were further identified by likelihood ratio test for ture QTL.
Details
Package: | mrMLM.GUI |
Type: | Package |
Version: | 4.0.2 |
Date: | 2020-10-8 |
Depends: | shiny,lars |
Imports: | methods,foreach,ncvreg,coin,sampling,data.table,doParallel,shinyjs,bigmemory,mrMLM |
License: | GPL version 2 or newer |
LazyLoad: | yes |
Users can use library(mrMLM.GUI) to start the GUI and use 'mrMLM.GUI()' to restart the programe.
Author(s)
Zhang Ya-Wen, Li Pei, Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
References
1. Zhang YM, Mao Y, Xie C, Smith H, Luo L, Xu S*. Genetics 2005,169:2267-2275. 2. Wang SB, Feng JY, Ren WL, Huang B, Zhou L, Wen YJ, et al. Sci Rep 2016,6:19444. 3. Tamba CL, Ni YL, Zhang YM*. PLoS Comput Biol 2017,13(1):e1005357. 4. Zhang J, Feng JY, Ni YL, Wen YJ, Niu Y, Tamba CL, et al. Heredity 2018,118(6):517-524. 5. Ren WL, Wen YJ, Dunwell JM, Zhang YM*. Heredity 2018,120(3): 208-218. 6. Wen YJ, Zhang H, Ni YL, Huang B, Zhang J, Feng JY, et al. Brief Bioinform 2018,19(4):700-712. 7. Tamba CL, Zhang YM. bioRxiv,preprint first posted online Jun. 7, 2018, doi:https://doi.org/10.1101/341784. 8. Zhang YW, Tamba CL, Wen YJ, Li P, Ren WL, Ni YL, et al. Genomics, Proteomics & Bioinformatics, Accept.
Examples
## Not run: mrMLM.GUI()
To perform GWAS with FASTmrEMMA method
Description
FAST multi-locus random-SNP-effect EMMA
Usage
FASTmrEMMA(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,Likelihood,CLO)
Arguments
gen |
genotype matrix. |
phe |
phenotype matrix. |
outATCG |
genotype for code 1. |
genRaw |
raw genotype. |
kk |
kinship matrix. |
psmatrix |
population structure matrix. |
svpal |
Critical P-value for selecting variable. |
svmlod |
Critical LOD score for significant QTN. |
Genformat |
Format for genotypic codes. |
Likelihood |
restricted maximum likelihood (REML) and maximum likelihood (ML). |
CLO |
number of CPU. |
Author(s)
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G1=data(fmegen)
P1=data(mrphe)
G2=data(fmegenraw)
result=FASTmrEMMA(fmegen,mrphe,outATCG=NULL,fmegenraw,kk=NULL,
psmatrix=NULL,0.005,3,1,Likelihood="REML",CLO=1)
To perform GWAS with FASTmrMLM method
Description
FAST multi-locus random-SNP-effect Mixed Linear Model
Usage
FASTmrMLM(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svrad,svmlod,Genformat,CLO)
Arguments
gen |
genotype matrix. |
phe |
phenotype matrix. |
outATCG |
genotype for code 1. |
genRaw |
raw genotype. |
kk |
kinship matrix. |
psmatrix |
population structure matrix. |
svpal |
Critical P-value for selecting variable. |
svrad |
Search Radius in search of potentially associated QTN. |
svmlod |
Critical LOD score for significant QTN. |
Genformat |
Format for genotypic codes. |
CLO |
number of CPU. |
Author(s)
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G1=data(mrgen)
P1=data(mrphe)
G2=data(mrgenraw)
result=FASTmrMLM(mrgen,mrphe,outATCG=NULL,mrgenraw,kk=NULL,psmatrix=NULL,
0.01,20,3,1,CLO=1)
To perform GWAS with ISIS EM-BLASSO method
Description
Iterative Sure Independence Screening EM-Bayesian LASSO
Usage
ISIS(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,CLO)
Arguments
gen |
genotype matrix. |
phe |
phenotype matrix. |
outATCG |
genotype for code 1. |
genRaw |
raw genotype. |
kk |
kinship matrix. |
psmatrix |
population structure matrix. |
svpal |
Critical P-value for selecting variable. |
svmlod |
Critical LOD score for significant QTN. |
Genformat |
Format for genotypic codes. |
CLO |
number of CPU. |
Author(s)
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G1=data(mrgen)
P1=data(mrphe)
G2=data(mrgenraw)
result=ISIS(mrgen,mrphe,outATCG=NULL,mrgenraw,kk=NULL,psmatrix=NULL,
0.01,3,1,CLO=1)
Genotype data
Description
Numeric format of genotype dataset.
Usage
data(fmegen)
Details
Dataset input of Genotype for FASTmrEMMA function.
Author(s)
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
raw genotype data
Description
Numeric format of raw genotype dataset.
Usage
data(fmegenraw)
Details
Dataset input of raw genotype for FASTmrEMMA function.
Author(s)
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
To perform GWAS with mrMLM method
Description
multi-locus random-SNP-effect Mixed Linear Model
Usage
mrMLMFun(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svrad,svmlod,Genformat,CLO)
Arguments
gen |
genotype matrix. |
phe |
phenotype matrix. |
outATCG |
genotype for code 1. |
genRaw |
raw genotype. |
kk |
kinship matrix. |
psmatrix |
population structure matrix. |
svpal |
Critical P-value for selecting variable |
svrad |
Search Radius in search of potentially associated QTN. |
svmlod |
Critical LOD score for significant QTN. |
Genformat |
Format for genotypic codes. |
CLO |
number of CPU. |
Author(s)
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G1=data(mrgen)
P1=data(mrphe)
G2=data(mrgenraw)
result=mrMLMFun(mrgen,mrphe,outATCG=NULL,mrgenraw,kk=NULL,psmatrix=NULL,
0.01,20,3,1,CLO=1)
Genotype data
Description
Numeric format of genotype dataset.
Usage
data(mrgen)
Details
Dataset input of Genotype for mrMLM function.
Author(s)
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
raw genotype data
Description
Numeric format of raw genotype dataset.
Usage
data(mrgenraw)
Details
Dataset input of raw genotype for mrMLM function.
Author(s)
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
phenotype data
Description
phenotype dataset.
Usage
data(mrphe)
Details
Dataset input of phenotype for mrMLM function.
Author(s)
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
Matrix multiplication acceleration algorithm.
Description
Matrix multiplication acceleration algorithm.
Usage
multiplication_speed(A,B)
Arguments
A |
matrix A. |
B |
matrix B. |
Author(s)
Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
## Not run:
A<-matrix(1:10,2,5)
B<-matrix(1:10,5:2)
result<-multiplication_speed(A,B)
## End(Not run)
To perform GWAS with pKWmEB method
Description
Kruskal-Wallis test with empirical Bayes under polygenic background control
Usage
pKWmEB(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,CLO)
Arguments
gen |
genotype matrix. |
phe |
phenotype matrix. |
outATCG |
genotype for code 1. |
genRaw |
raw genotype. |
kk |
kinship matrix. |
psmatrix |
population structure matrix. |
svpal |
Critical P-value for selecting variable. |
svmlod |
Critical LOD score for significant QTN. |
Genformat |
Format for genotypic codes. |
CLO |
number of CPU. |
Author(s)
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G1=data(mrgen)
P1=data(mrphe)
G2=data(mrgenraw)
result=pKWmEB(mrgen,mrphe,outATCG=NULL,mrgenraw,kk=NULL,psmatrix=NULL,
0.05,3,1,CLO=1)
To perform GWAS with pLARmEB method
Description
polygene-background-control-based least angle regression plus Empirical Bayes
Usage
pLARmEB(gen,phe,outATCG,genRaw,kk,psmatrix,CriLOD,lars1,Genformat,Bootstrap,CLO)
Arguments
gen |
genotype matrix. |
phe |
phenotype matrix. |
outATCG |
genotype for code 1. |
genRaw |
raw genotype. |
kk |
kinship matrix. |
psmatrix |
population structure matrix. |
CriLOD |
Critical LOD score for significant QTN. |
lars1 |
No. of potentially associated variables selected by LARS. |
Genformat |
Format for genotypic codes. |
Bootstrap |
Bootstrap=FALSE indicates the analysis of only real dataset, Bootstrap=TRUE indicates the analysis of both real dataset and four resampling datasets. |
CLO |
number of CPU. |
Author(s)
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>
Examples
G1=data(mrgen)
P1=data(mrphe)
G2=data(mrgenraw)
result=pLARmEB(mrgen,mrphe,outATCG=NULL,mrgenraw,kk=NULL,psmatrix=NULL,
3,20,1,Bootstrap=FALSE,CLO=1)