\name{GenABEL-package}
\alias{GenABEL-package}
\alias{GenABEL}
\docType{package}
\title{
GenABEL: an R package for Genome Wide Association Analysis
}
\description{

Genome-wide association (GWA) analysis is a tool of choice for identification of genes for complex traits. Effective storage, handling and analysis of GWA data represent a challenge to modern computa-tional genetics. GWA studies generate large amount of data: hun-dreds of thousands of single nucleotide polymorphisms (SNPs) are genotyped in hundreds or thousands of patients and controls. Data on each SNP undergoes several types of analysis: characterization of frequency distribution, testing of Hardy-Weinberg equilibrium, analysis of association between single SNPs and haplotypes and different traits, and so on. Because SNP genotypes in dense marker sets are correlated, significance testing in GWA analysis is pref-erably performed using computationally intensive permutation test procedures, further increasing the com-putational burden.

To make GWA analysis possible on standard desktop computers we developed GenABEL library which addresses the following objectives: 

(1) Minimisation of the amount of rapid access memory (RAM) used and the time required for data transactions. For this, we developed an effective data storage and manipulation model.

(2) Maximisation of the throughput of GWA analysis. For this, we designed optimal fast procedures for specific genetic tests. 

Imbedding GenABEL into R environment allows for easy data characterisation, exploration and presentation of the results and gives access to a wide range of standard and special statistical analysis functions available in base R and specific R packages, such as "haplo.stats", "genetics", etc.
}
\details{
\tabular{ll}{
Package: \tab GenABEL\cr
Type: \tab Package\cr
Version: \tab 1.4-0c\cr
Date: \tab 2008-07-25\cr
License: \tab GPL (>= 2)\cr
}

To see (more or less complete) functionality of GenABEL, try running

demo(ge03d2).

Other demo of interest could be run with demo(srdta). 
Depending on your user priveleges in Windows, it may well not run. In this
case, try demo(srdtawin).

The most important functions and classes are:

For converting data from other formats, see
\code{\link{convert.snp.illumina}} (Illumina/Affymetrix-like format). This is 
our preferred converting function, very extensively tested. Other conversion 
functions include:  
\code{\link{convert.snp.text}} (conversion from human-readable GenABEL format),
\code{\link{convert.snp.ped}} (Linkage, Merlin, Mach, and similar files),
\code{\link{convert.snp.mach}} (Mach-format),
\code{\link{convert.snp.tped}} (from PLINK TPED format),
\code{\link{convert.snp.affymetrix}} (BRML-style files).

To load the data, see \code{\link{load.gwaa.data}}.

For data managment and manipulations see
\code{\link{merge.gwaa.data}},
\code{\link{merge.snp.data}},
\code{\link{gwaa.data-class}},
\code{\link{snp.data-class}},
\code{\link{snp.names}},
\code{\link{snp.subset}}.

%For merging objects of \code{\link{gwaa.data-class}}, see \code{\link{merge.gwaa.data}}.

For merging extra data to the phenotypic part of \code{\link{gwaa.data-class}} object, 
see \code{\link{add.phdata}}.

For traits manipulations see 
\code{\link{ztransform}} (transformation to standard Normal),
\code{\link{rntransform}} (rank-transformation to normality),
\code{\link{npsubtreated}} (non-parametric routine to "impute" trait's values in these medicated).


For quality control, see
\code{\link{check.trait}},
\code{\link{check.marker}},
\code{\link{HWE.show}},
\code{\link{summary.snp.data}},
\code{\link{perid.summary}},
\code{\link{ibs}},
\code{\link{hom}}.

For fast analysis function, see
\code{\link{scan.gwaa-class}},
\code{\link{ccfast}},
\code{\link{qtscore}},
\code{\link{mmscore}},
\code{\link{egscore}},
\code{\link{ibs}},
\code{\link{r2fast}},
\code{\link{dprfast}},
\code{\link{rhofast}}

For specific tools facilitating analysis of the data with stratification
(population stratification or (possibly unknown) pedigree structure), see
\code{\link{qtscore}} (implements basic Genomic Control),
\code{\link{ibs}} (computations of IBS / genomic IBD),
\code{\link{egscore}} (stratification adjustment following Price et al.),
\code{\link{polygenic}} (heritability analysis),
\code{\link{mmscore}} (score test of Chen and Abecasis),
\code{\link{grammar}} (grammar test of Aulchenko et al.).

For functions facilitating construction of tables for your manuscript, see
\code{\link{descriptives.marker}},
\code{\link{descriptives.trait}},
\code{\link{descriptives.scan}}.

For meta-analysis and related, see help on
\code{\link{formetascore}}.

For link to WEB databases, see
\code{\link{show.ncbi}}.

For interfaces to other packages and standard R functions, 
also for 2D scans, see
\code{\link{scan.glm}},
\code{\link{scan.glm.2D}},
\code{\link{scan.haplo}},
\code{\link{scan.haplo.2D}},
\code{\link{scan.gwaa-class}},
\code{\link{scan.gwaa.2D-class}}.

For graphical facilities, see
\code{\link{plot.scan.gwaa}},
\code{\link{plot.check.marker}}.

}
\author{
Yurii Aulchenko

Maintainer: Yurii Aulchenko <i.aoultchenko@erasmusmc.nl>
}
\references{
If you use GenABEL package in your analysis, please cite the following work:

Aulchenko Y.S., Ripke S., Isaacs A., van Duijn C.M. GenABEL: an R package 
for genome-wide association analysis. Bioinformatics. 2007 23(10):1294-6.

If you used \code{\link{polygenic}}, please cite

Thompson EA, Shaw RG (1990) Pedigree analysis for quantitative 
traits: variance components without matrix inversion. Biometrics 
46, 399-413.

If you used environmental residuals from \code{\link{polygenic}} for 
\code{\link{qtscore}}, used GRAMMAR and/or GRAMMAS analysis, please cite

Aulchenko YS, de Koning DJ, Haley C. Genomewide rapid association using mixed model 
and regression: a fast and simple method for genome-wide pedigree-based quantitative 
trait loci association analysis. Genetics. 2007 177(1):577-85.

Amin N, van Duijn CM, Aulchenko YS. A genomic background based method for 
association analysis in related individuals. PLoS ONE. 2007 Dec 5;2(12):e1274. 

If you used \code{\link{mmscore}}, please cite

Chen WM, Abecasis GR. Family-based association tests for genome-wide association 
scans. Am J Hum Genet. 2007 Nov;81(5):913-26. 

For exact HWE (used in \code{\link{summary.snp.data}}), please cite:

Wigginton G.E., Cutler D.J., Abecasis G.R. A note on exact tests of 
Hardy-Weinberg equilibrium. Am J Hum Genet. 2005 76: 887-893.

For haplo.stats (\code{\link{scan.haplo}}, \code{\link{scan.haplo.2D}}), please cite:

Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. Score tests for 
association between traits and haplotypes when linkage phase is ambiguous. 
Am J Hum Genet. 2002 70:425-434.

For fast LD computations (function \code{\link{dprfast}}, \code{\link{r2fast}}), please cite:

Hao K, Di X, Cawley S. LdCompare: rapid computation of single- and 
multiple-marker r2 and genetic coverage. Bioinformatics. 2006 23:252-254.

If you used \code{\link{npsubtreated}}, please cite

Levy D, DeStefano AL, Larson MG, O'Donnell CJ, Lifton RP, Gavras H, Cupples LA, 
Myers RH. Evidence for a gene influencing blood pressure on chromosome 17. 
Genome scan linkage results for longitudinal blood pressure phenotypes in 
subjects from the framingham heart study. Hypertension. 2000 Oct;36(4):477-83.
}
\keyword{package}
\seealso{
Packages \code{genetics},
\code{haplo.stats},
\code{qvalue},
}
\examples{
	\dontrun{
	demo(ge03d2)
	demo(srdta)
	demo(srdtawin)
	}
}
