mrMLM.GUI-package: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for...

In mrMLM.GUI: 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<[e-mail]>

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() 

Example output

Loading required package: shiny
Loading required package: lars
Loaded lars 1.2

mrMLM.GUI documentation built on Oct. 23, 2020, 8:13 p.m.