[Genabel-commits] r940 - in pkg/GenABEL: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Aug 15 16:37:54 CEST 2012
Author: yurii
Date: 2012-08-15 16:37:54 +0200 (Wed, 15 Aug 2012)
New Revision: 940
Added:
pkg/GenABEL/R/GenABEL.R
pkg/GenABEL/man/GenABEL.Rd
pkg/GenABEL/man/grammar.Rd
Removed:
pkg/GenABEL/R/GenABEL-package.R
pkg/GenABEL/man/GenABEL-package.Rd
Modified:
pkg/GenABEL/CHANGES.LOG
pkg/GenABEL/DESCRIPTION
pkg/GenABEL/R/check.trait.R
pkg/GenABEL/R/convert.snp.mach.R
pkg/GenABEL/generate_documentation.R
Log:
Small updates to documentation
Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG 2012-08-10 17:28:09 UTC (rev 939)
+++ pkg/GenABEL/CHANGES.LOG 2012-08-15 14:37:54 UTC (rev 940)
@@ -1,9 +1,15 @@
-(2012.08.09)
+(2012.08.15, YA)
+Small updates to documentation, verifying that checks are passed.
+Many NOTEs about use of partial arguments - something to fix
+eventually.
+
+(2012.08.09, YT)
+
Add new function GC (Genomic control for non-additive models) and GC_ovdom fot overdominant model.
Update some functions.
-(2012.07.06)
+(2012.07.06, YT)
Removed documentation file grammar.old.Rd as obsolete
Add new function PGC (Polynomial genomic control for non-additive models)
Modified: pkg/GenABEL/DESCRIPTION
===================================================================
--- pkg/GenABEL/DESCRIPTION 2012-08-10 17:28:09 UTC (rev 939)
+++ pkg/GenABEL/DESCRIPTION 2012-08-15 14:37:54 UTC (rev 940)
@@ -4,7 +4,7 @@
Version: 1.7-1
Date: 2012-01-11
Author: GenABEL developers
-Maintainer: GenABEL developers <genabel.project at gmail.com>
+Maintainer: GenABEL project <genabel.project at gmail.com>
Depends: R (>= 2.10.0), methods, MASS, utils
Suggests: qvalue, genetics, haplo.stats, DatABEL (>= 0.9-0),
hglm, MetABEL, PredictABEL, VariABEL
Deleted: pkg/GenABEL/R/GenABEL-package.R
===================================================================
--- pkg/GenABEL/R/GenABEL-package.R 2012-08-10 17:28:09 UTC (rev 939)
+++ pkg/GenABEL/R/GenABEL-package.R 2012-08-15 14:37:54 UTC (rev 940)
@@ -1,212 +0,0 @@
-#' GenABEL: an R package for Genome Wide Association Analysis
-#'
-#' 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 computational genetics. GWA studies
-#' generate large amount of data: hundreds 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 preferably performed
-#' using computationally intensive permutation test procedures,
-#' further increasing the computational burden.
-#'
-#' To make GWA analysis possible on standard desktop computers
-#' we developed GenABEL library which addresses the following
-#' objectives:
-#'
-#' (1) Minimization 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) Maximization of the throughput of GWA analysis. For this,
-#' we designed optimal fast procedures for specific genetic tests.
-#'
-#' Embedding GenABEL into R environment allows for easy data
-#' characterization, 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.
-#'
-#' 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).
-#'
-#' For converting of GenABEL's data to other formats, see
-#' \code{\link{export.merlin}} (MERLIN and MACH formats),
-#' \code{\link{export.impute}} (IMPUTE, SNPTEST and CHIAMO formats),
-#' \code{\link{export.plink}} (PLINK format, also exports phenotypic data).
-#'
-#' To load the data, see \code{\link{load.gwaa.data}}.
-#'
-#' For conversion to DatABEL format (used by ProbABEL and some other
-#' GenABEL suite packages), see
-#' \code{\link{impute2databel}},
-#' \code{\link{impute2mach}},
-#' \code{\link{mach2databel}}.
-#'
-#' 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 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}} (estimate linkage disequilibrium using R2),
-#' \code{\link{dprfast}} (estimate linkage disequilibrium using D'),
-#' \code{\link{rhofast}} (estimate linkage disequilibrium using 'rho')
-#'
-#' 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{polygenic_hglm}} (another function for 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 functions recunstructing relationships from genomic data,
-#' see
-#' \code{\link{findRelatives}}, \code{\link{reconstructNPs}}.
-#'
-#' 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}}.
-#'
-#' @aliases GenABEL-package GenABEL
-#'
-#' @author Yurii Aulchenko et al.
-#' (see help pages for specific functions)
-#'
-#' @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.
-#'
-#' @keywords package
-#'
-#' @seealso \code{DatABEL}, \code{genetics}, \code{haplo.stats}, \code{qvalue}
-#'
-#' @examples
-#' \dontrun{
-#' demo(ge03d2)
-#' demo(srdta)
-#' demo(srdtawin)
-#' }
-#'
-
-"GenABEL-package" <- function() {}
\ No newline at end of file
Copied: pkg/GenABEL/R/GenABEL.R (from rev 939, pkg/GenABEL/R/GenABEL-package.R)
===================================================================
--- pkg/GenABEL/R/GenABEL.R (rev 0)
+++ pkg/GenABEL/R/GenABEL.R 2012-08-15 14:37:54 UTC (rev 940)
@@ -0,0 +1,215 @@
+#' GenABEL: an R package for Genome Wide Association Analysis
+#'
+#' 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 computational genetics. GWA studies
+#' generate large amount of data: hundreds 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 preferably performed
+#' using computationally intensive permutation test procedures,
+#' further increasing the computational burden.
+#'
+#' To make GWA analysis possible on standard desktop computers
+#' we developed GenABEL library which addresses the following
+#' objectives:
+#'
+#' (1) Minimization 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) Maximization of the throughput of GWA analysis. For this,
+#' we designed optimal fast procedures for specific genetic tests.
+#'
+#' Embedding GenABEL into R environment allows for easy data
+#' characterization, 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.
+#'
+#' 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).
+#'
+#' For converting of GenABEL's data to other formats, see
+#' \code{\link{export.merlin}} (MERLIN and MACH formats),
+#' \code{\link{export.impute}} (IMPUTE, SNPTEST and CHIAMO formats),
+#' \code{\link{export.plink}} (PLINK format, also exports phenotypic data).
+#'
+#' To load the data, see \code{\link{load.gwaa.data}}.
+#'
+#' For conversion to DatABEL format (used by ProbABEL and some other
+#' GenABEL suite packages), see
+#' \code{\link{impute2databel}},
+#' \code{\link{impute2mach}},
+#' \code{\link{mach2databel}}.
+#'
+#' 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 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}} (estimate linkage disequilibrium using R2),
+#' \code{\link{dprfast}} (estimate linkage disequilibrium using D'),
+#' \code{\link{rhofast}} (estimate linkage disequilibrium using 'rho')
+#'
+#' 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{polygenic_hglm}} (another function for 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 functions recunstructing relationships from genomic data,
+#' see
+#' \code{\link{findRelatives}}, \code{\link{reconstructNPs}}.
+#'
+#' 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 et al.
+#' (see help pages for specific functions)
+#'
+#' @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.
+#'
+#' @keywords package
+#'
+#' @seealso \code{DatABEL}, \code{genetics}, \code{haplo.stats}, \code{qvalue}
+#'
+#' @examples
+#' \dontrun{
+#' demo(ge03d2)
+#' demo(srdta)
+#' demo(srdtawin)
+#' }
+#'
+#' @name GenABEL
+#' @docType package
+#' @title GWAS in R
+#' @aliases GenABEL genabel
+#' @keywords package
+#'
+NULL
\ No newline at end of file
Modified: pkg/GenABEL/R/check.trait.R
===================================================================
--- pkg/GenABEL/R/check.trait.R 2012-08-10 17:28:09 UTC (rev 939)
+++ pkg/GenABEL/R/check.trait.R 2012-08-15 14:37:54 UTC (rev 940)
@@ -28,7 +28,7 @@
tt <- tra[seq(1:(length(tra)-1))]
muj <- mean(tt,na.rm=TRUE)
rvarj <- 1./var(tt,na.rm=TRUE)
- Pv[j] = pchisq((tra[j]-muj)*(tra[j]-muj)*rvarj,1,lower=F)
+ Pv[j] = pchisq((tra[j]-muj)*(tra[j]-muj)*rvarj,1,lower.tail = FALSE)
}
}
cat("--------------------------------\n")
@@ -36,7 +36,7 @@
cat("Missing:",sum(is.na(get(trait[i]))),"(",100*sum(is.na(get(trait[i])))/length(get(trait[i])),"%)\n");
cat("Mean =",mean(get(trait[i]),na.rm=TRUE),"; s.d. =",sqrt(var(get(trait[i]),na.rm=TRUE)),"\n");
if (min(Pv,na.rm=TRUE)<fdrate) {
- qobj<-qvaluebh95(Pv,fdr = fdrate)
+ qobj<-qvaluebh95(Pv,fdrate = fdrate)
if (sum(qobj$signif)>=1) {
cat("Outliers discovered for trait",trait[i],":\n");
cat(data$id[qobj$signif])
Modified: pkg/GenABEL/R/convert.snp.mach.R
===================================================================
--- pkg/GenABEL/R/convert.snp.mach.R 2012-08-10 17:28:09 UTC (rev 939)
+++ pkg/GenABEL/R/convert.snp.mach.R 2012-08-15 14:37:54 UTC (rev 940)
@@ -7,14 +7,14 @@
cat("****************************************\n")
cat("Converting data to raw format...\n")
- convert.snp.ped(pedf=pedfile,mapf=mapfile,outf=outfile,format="mach", wslash=T, strand=strand, ... )
+ convert.snp.ped(pedfile=pedfile,mapfile=mapfile,outfile=outfile,format="mach", wslash=T, strand=strand, ... )
if (quality<=0) {
cat("No quality filtering - Done.\n")
return(invisible(0))
}
cat("Reading info-file...\n")
- info <- read.table(file=infofile,head=T)
+ info <- read.table(file=infofile,header=TRUE)
ncols <- dim(info)[2]
if (ncols!=7) stop("Wrong number of columns in info-file")
nrows <- dim(info)[1]
@@ -23,7 +23,7 @@
cat("Loading raw data...\n")
ifile <- file(outfile,"r")
header <- scan(file=ifile,what=character(),nlines=1,quiet=TRUE)
- vver <- grep(x=header,pat="version")
+ vver <- grep(x=header,pattern="version")
if (length(vver)>0) {ver <- as.numeric(header[vver+1]);} else {ver <- 0;}
if (is.na(ver)) warning("Incorrect data format version number")
if (ver > 0) {ids <- scan(file=ifile,what=character(),nlines=1,quiet=TRUE);}
@@ -67,7 +67,7 @@
npsd<-table(pass)["FALSE"]
cat("SNP filtering done --",psd,"passed quality threshold,",npsd,"did not pass...\n")
cat("Writing data...\n")
- save.snp.data(a,genof=outfile,human=FALSE)
+ save.snp.data(a,genofile=outfile,human=FALSE)
return(invisible(0))
}
Modified: pkg/GenABEL/generate_documentation.R
===================================================================
--- pkg/GenABEL/generate_documentation.R 2012-08-10 17:28:09 UTC (rev 939)
+++ pkg/GenABEL/generate_documentation.R 2012-08-15 14:37:54 UTC (rev 940)
@@ -12,7 +12,7 @@
"findRelatives.R",
"GC.R",
"GC_ovdom.R",
- "GenABEL-package.R",
+ "GenABEL.R",
"generateOffspring.R",
"getLogLikelihoodGivenRelation.R",
"grammar.R",
@@ -40,6 +40,7 @@
unlink("GenABEL",recursive=TRUE)
package.skeleton("GenABEL",code_files=roxy_files)
roxygenize("GenABEL",roxygen.dir="GenABEL",copy=F,unlink=F)
+unlink("GenABEL/man/GenABEL-package.Rd",recursive=TRUE)
lstf <- paste("GenABEL/man/",list.files("GenABEL/man/"),sep="")
lstf
file.copy(lstf,"../man/",overwrite=TRUE)
Deleted: pkg/GenABEL/man/GenABEL-package.Rd
===================================================================
--- pkg/GenABEL/man/GenABEL-package.Rd 2012-08-10 17:28:09 UTC (rev 939)
+++ pkg/GenABEL/man/GenABEL-package.Rd 2012-08-15 14:37:54 UTC (rev 940)
@@ -1,235 +0,0 @@
-\name{GenABEL-package}
-\alias{GenABEL}
-\alias{GenABEL-package}
-\title{GenABEL: an R package for Genome Wide Association Analysis}
-\usage{
- GenABEL-package()
-}
-\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 computational genetics.
- GWA studies generate large amount of data: hundreds 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 preferably performed using
- computationally intensive permutation test procedures,
- further increasing the computational burden.
-}
-\details{
- To make GWA analysis possible on standard desktop
- computers we developed GenABEL library which addresses
- the following objectives:
-
- (1) Minimization 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) Maximization of the throughput of GWA analysis. For
- this, we designed optimal fast procedures for specific
- genetic tests.
-
- Embedding GenABEL into R environment allows for easy data
- characterization, 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.
-
- 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).
-
- For converting of GenABEL's data to other formats, see
- \code{\link{export.merlin}} (MERLIN and MACH formats),
- \code{\link{export.impute}} (IMPUTE, SNPTEST and CHIAMO
- formats), \code{\link{export.plink}} (PLINK format, also
- exports phenotypic data).
-
- To load the data, see \code{\link{load.gwaa.data}}.
-
- For conversion to DatABEL format (used by ProbABEL and
- some other GenABEL suite packages), see
- \code{\link{impute2databel}}, \code{\link{impute2mach}},
- \code{\link{mach2databel}}.
-
- 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 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}} (estimate linkage disequilibrium
- using R2), \code{\link{dprfast}} (estimate linkage
- disequilibrium using D'), \code{\link{rhofast}} (estimate
- linkage disequilibrium using 'rho')
-
- 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{polygenic_hglm}}
- (another function for 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 functions recunstructing relationships from genomic
- data, see \code{\link{findRelatives}},
- \code{\link{reconstructNPs}}.
-
- 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}}.
-}
-\examples{
-\dontrun{
-demo(ge03d2)
-demo(srdta)
-demo(srdtawin)
-}
-}
-\author{
- Yurii Aulchenko et al. (see help pages for specific
- functions)
-}
-\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.
-}
-\seealso{
- \code{DatABEL}, \code{genetics}, \code{haplo.stats},
- \code{qvalue}
-}
-\keyword{package}
-
Added: pkg/GenABEL/man/GenABEL.Rd
===================================================================
--- pkg/GenABEL/man/GenABEL.Rd (rev 0)
+++ pkg/GenABEL/man/GenABEL.Rd 2012-08-15 14:37:54 UTC (rev 940)
@@ -0,0 +1,237 @@
+\docType{package}
+\name{GenABEL}
+\alias{GenABEL}
+\alias{GenABEL-package}
+\alias{genabel}
+\title{GWAS in R}
+\description{
+ GenABEL: an R package for Genome Wide Association
+ Analysis
+}
+\details{
+ 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 computational genetics.
+ GWA studies generate large amount of data: hundreds 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 preferably performed using
+ computationally intensive permutation test procedures,
+ further increasing the computational burden.
+
+ To make GWA analysis possible on standard desktop
+ computers we developed GenABEL library which addresses
+ the following objectives:
+
[TRUNCATED]
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svnlook diff /svnroot/genabel -r 940
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