| Title: | Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for Genome-Wide Association Study with Graphical User Interface |
|---|---|
| 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>. |
| Authors: | Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming |
| Maintainer: | Yuanming Zhang<[email protected]> |
| License: | GPL (>= 2) |
| Version: | 4.0.2 |
| Built: | 2025-03-17 03:48:44 UTC |
| Source: | https://github.com/cran/mrMLM.GUI |
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.
| 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.
Zhang Ya-Wen, Li Pei, Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[email protected]>
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.
## Not run: mrMLM.GUI()## Not run: mrMLM.GUI()
FAST multi-locus random-SNP-effect EMMA
FASTmrEMMA(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,Likelihood,CLO)FASTmrEMMA(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,Likelihood,CLO)
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. |
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[email protected]>
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)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)
FAST multi-locus random-SNP-effect Mixed Linear Model
FASTmrMLM(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svrad,svmlod,Genformat,CLO)FASTmrMLM(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svrad,svmlod,Genformat,CLO)
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. |
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[email protected]>
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)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)
Numeric format of genotype dataset.
data(fmegen)data(fmegen)
Dataset input of Genotype for FASTmrEMMA function.
Maintainer: Yuan-Ming Zhang<[email protected]>
Numeric format of raw genotype dataset.
data(fmegenraw)data(fmegenraw)
Dataset input of raw genotype for FASTmrEMMA function.
Maintainer: Yuan-Ming Zhang<[email protected]>
Iterative Sure Independence Screening EM-Bayesian LASSO
ISIS(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,CLO)ISIS(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,CLO)
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. |
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[email protected]>
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)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)
Numeric format of genotype dataset.
data(mrgen)data(mrgen)
Dataset input of Genotype for mrMLM function.
Maintainer: Yuan-Ming Zhang<[email protected]>
Numeric format of raw genotype dataset.
data(mrgenraw)data(mrgenraw)
Dataset input of raw genotype for mrMLM function.
Maintainer: Yuan-Ming Zhang<[email protected]>
multi-locus random-SNP-effect Mixed Linear Model
mrMLMFun(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svrad,svmlod,Genformat,CLO)mrMLMFun(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svrad,svmlod,Genformat,CLO)
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. |
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[email protected]>
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)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)
phenotype dataset.
data(mrphe)data(mrphe)
Dataset input of phenotype for mrMLM function.
Maintainer: Yuan-Ming Zhang<[email protected]>
Matrix multiplication acceleration algorithm.
multiplication_speed(A,B)multiplication_speed(A,B)
A |
matrix A. |
B |
matrix B. |
Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, and Zhang Yuan-Ming
Maintainer: Yuanming Zhang<[email protected]>
## Not run: A<-matrix(1:10,2,5) B<-matrix(1:10,5:2) result<-multiplication_speed(A,B) ## End(Not run)## Not run: A<-matrix(1:10,2,5) B<-matrix(1:10,5:2) result<-multiplication_speed(A,B) ## End(Not run)
Kruskal-Wallis test with empirical Bayes under polygenic background control
pKWmEB(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,CLO)pKWmEB(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,CLO)
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. |
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[email protected]>
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)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)
polygene-background-control-based least angle regression plus Empirical Bayes
pLARmEB(gen,phe,outATCG,genRaw,kk,psmatrix,CriLOD,lars1,Genformat,Bootstrap,CLO)pLARmEB(gen,phe,outATCG,genRaw,kk,psmatrix,CriLOD,lars1,Genformat,Bootstrap,CLO)
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. |
Zhang Ya-Wen, Li Pei, and Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[email protected]>
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)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)