注册 登录  
 加关注
   显示下一条  |  关闭
温馨提示!由于新浪微博认证机制调整,您的新浪微博帐号绑定已过期,请重新绑定!立即重新绑定新浪微博》  |  关闭

wangyufeng的博客

祝愿BB 健康开心快乐每一天

 
 
 

日志

 
 

Funmap:Functional Mapping Package for R (Version 2.0)  

2011-10-17 20:14:26|  分类: 数量遗传学 |  标签: |举报 |字号 订阅

  下载LOFTER 我的照片书  |
Description:
The Funmap package is developed to identify quantitative trait loci (QTL) for a longitudinal, or vectorized, phenotypic trait as based on the Funmap model[1]. Version 2.0 has implemented 6 functional curves( Logistic Curve, Bi-Exponential Curve, Pharmacology Curve, Nonparametric method, Segmental Lines and Compisite Model) and three cross types(backcross, F2 cross and RILs by selfing). the Function FM.one_step is the easiest way to call the computational model by five arguments of the marker file, the genotype file, the phenotype file, the curve type and the cross type. The computational model automatically performs the hypothesis tests and permutation. The package can output a brief report for the raw data, results of the hypothesis tests and permutation results. For some results, figures will be outputted to a PDF file and a CSV file will be generated. For more details, please refer to the document.

[1] Ma, C. X., G. Casella, and R. L. Wu, 2003. Functional mapping of quantitative trait loci underlying the character process: A theoretical framework. Genetics 161(4): 1751-1762.


Download:
The packages for Windows, Linux and Mac OS are available. The document also can be downloaded by the following link.

Introduction for the Funmap Package (01/18/2011)
R package for Linux and Mac, version 2.0 (01/24/2011, 146 KB)
R package for windows, version 2.0 (01/24/2011, 319 KB)

Installation:
The Funmap package depends on the MSBVar package (available on CRAN), so this package should be installed first. To install Funmap, download the package file and type the appropriate command below or click the menu item "Install packages from local zip files".

Windows OS:

>install.packages("x:/fullpath/Funmap_2.0.zip", repos=NULL)

Linux/Mac OS:

>install.packages("/fullpath/ Funmap_2.0.tar.gz", repos=NULL)

Before the package is used in R, the package importation is necessary by the following command:

> library(Funmap)

After it is loaded, all functions within Funmap will be readily available to the user.


Sample Script:
The following source shows how to call the main function in R.
> library(Funmap);
> FM.one_step( "pheno.csv", "geno.csv", "marker.csv", MODEL_LC, CROSS_BC );

The following source shows how to call the main function in R.
> library(Funmap);
> FM.simu_test( MODEL_NP, CROSS_F2 );

The following source shows how to call the main function in R.
> library(Funmap);
> par <- FM.par( MODEL_NP, CROSS_RIL );
> dat <- FM.simulate(par);
> ret <- FM.hp_test(dat);
> FM.report( dat, ret, file="report.pdf" );

Sample Report:
Link: http://statgen.psu.edu/software/funmap/report_demo.pdf
Last updated:

Version 2.0  01/19/2011
Version 1.0  06/21/2010

via:http://statgen.psu.edu/software/funmap.html

  评论这张
 
阅读(783)| 评论(0)
推荐 转载

历史上的今天

在LOFTER的更多文章

评论

<#--最新日志,群博日志--> <#--推荐日志--> <#--引用记录--> <#--博主推荐--> <#--随机阅读--> <#--首页推荐--> <#--历史上的今天--> <#--被推荐日志--> <#--上一篇,下一篇--> <#-- 热度 --> <#-- 网易新闻广告 --> <#--右边模块结构--> <#--评论模块结构--> <#--引用模块结构--> <#--博主发起的投票-->
 
 
 
 
 
 
 
 
 
 
 
 
 
 

页脚

网易公司版权所有 ©1997-2017