SCM

R Development Page

Contributed R Packages

Below is a list of all packages provided by project GenABEL.

Important note for package binaries: R-Forge provides these binaries only for the most recent version of R, but not for older versions. In order to successfully install the packages provided on R-Forge, you have to switch to the most recent version of R or, alternatively, install from the package sources (.tar.gz).

Packages

DatABEL

file-based access to large matrices stored on HDD in binary format

  a package providing an interface to the C++ FILEVECTOR library facilitating analysis of large (giga- to tera-bytes) matrices; matrix storage is organized in a way that either columns or rows are quickly accessible; primarily aimed to support genome-wide association analyses e.g. using GenABEL, MixABEL and ProbABEL
  Version: 0.9-4 | Last change: 2014-04-02 17:57:31+02 | Rev.: 1670
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build | Stable Release: Get DatABEL 0.9-4 from CRAN
  R install command: install.packages("DatABEL", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


GenABEL

genome-wide SNP association analysis

  a package for genome-wide association analysis between quantitative or binary traits and single-nucleotide polymorphisms (SNPs).
  Version: 1.8-0 | Last change: 2014-07-01 06:47:21+02 | Rev.: 1759
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build | Stable Release: Get GenABEL 1.8-0 from CRAN
  R install command: install.packages("GenABEL", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


GenABEL.data

Package contains data which is used by GenABEL example and test functions

  GenABEL.data package consists of a number of data files used by GenABEL functions
  Version: 1.0.0 | Last change: 2013-12-09 10:14:48+01 | Rev.: 1460
  Download: linux(.tar.gz) | windows(.zip) | Build status: Current | Stable Release: Get GenABEL.data 1.0.0 from CRAN
  R install command: install.packages("GenABEL.data", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


MetABEL

Meta-analysis of genome-wide SNP association results

  A package for meta-analysis of genome-wide association scans between quantitative or binary traits and SNPs
  Version: 0.2-0 | Last change: 2014-02-03 16:54:11+01 | Rev.: 1586
  Download: linux(.tar.gz) | windows(.zip) | Build status: Current | Stable Release: Get MetABEL 0.2-0 from CRAN
  R install command: install.packages("MetABEL", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


MixABEL

mixed models for genetic association analysis

  a package for fast mixed models for association analysis in samples of related individuals
  Version: 0.1-2 | Last change: 2013-10-29 15:18:28+01 | Rev.: 1351
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build
  R install command: install.packages("MixABEL", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


PredictABEL

Assessment of risk prediction models

  PredictABEL includes functions to assess the performance of risk models. The package contains functions for the various measures that are used in empirical studies, including univariate and multivariate odds ratios (OR) of the predictors, the c-statistic (or area under the receiver operating characteristic (ROC) curve (AUC)), Hosmer-Lemeshow goodness of fit test, reclassification table, net reclassification improvement (NRI) and integrated discrimination improvement (IDI). Also included are functions to create plots, such as risk distributions, ROC curves, calibration plot, discrimination box plot and predictiveness curves. In addition to functions to assess the performance of risk models, the package includes functions to obtain weighted and unweighted risk scores as well as predicted risks using logistic regression analysis. These logistic regression functions are specifically written for models that include genetic variables, but they can also be applied to models that are based on non-genetic risk factors only. Finally, the package includes function to construct a simulated dataset with genotypes, genetic risks, and disease status for a hypothetical population, which is used for the evaluation of genetic risk models.
  Version: 1.2-2 | Last change: 2013-09-06 16:31:39+02 | Rev.: 1332
  Download: linux(.tar.gz) | windows(.zip) | Build status: Current | Stable Release: Get PredictABEL 1.2-1 from CRAN
  R install command: install.packages("PredictABEL", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


TestABEL

tests for GenABEL new stuff

  test stuff
  Version: 0.0-1 | Last change: 2013-11-04 11:03:00+01 | Rev.: 1359
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build
  R install command: install.packages("TestABEL", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)


VariABEL

Testing of genotypic variance heterogeneity to detect potentially interacting SNP.

  Presence of interaction between a SNP and another SNP (or another factor) can result in heterogeneity of variance between the genotypes of an interacting SNP. Detecting such heterogeneity gives prior knowledge for constructing a genetic model underlying complex trait.
  Version: 0.9-2 | Last change: 2014-02-14 08:58:43+01 | Rev.: 1610
  Download: linux(.tar.gz) | windows(.zip) | Build status: Failed to build | Stable Release: Get VariABEL 0.9-2 from CRAN
  R install command: install.packages("VariABEL", repos="http://R-Forge.R-project.org")
 
Logs:  
Package build: Source package (Linux x86_64) Windows binary (x86_64/i386)
Package check: Linux x86_64 (patched) | Linux x86_64 (devel) Windows (patched) | Windows (devel)

 

Build status codes

0 - Current: the package is available for download. The corresponding package passed checks on the Linux and Windows platform without ERRORs.
1 - Scheduled for build: the package has been recognized by the build system and provided in the staging area.
2 - Building: the package has been sent to the build machines. It will be built and checked using the latest patched version of R. Note that it is included in a batch of several packages. Thus, this process will take some time to finish.
3 - Failed to build: the package failed to build or did not pass the checks on the Linux and/or Windows platform. It is not made available since it does not meet the policies.
4 - Conflicts: two or more packages of the same name exist. None of them will be built. Maintainers are asked to negotiate further actions.
5 - Offline: the package is not available. The build system may be offline or the package maintainer did not trigger a rebuild (done e.g., via committing to the package repository).

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