[Genabel-commits] r1188 - in pkg/GenABEL: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 9 17:17:57 CEST 2013
Author: yurii
Date: 2013-04-09 17:17:56 +0200 (Tue, 09 Apr 2013)
New Revision: 1188
Modified:
pkg/GenABEL/R/cocohet.R
pkg/GenABEL/generate_documentation.R
pkg/GenABEL/man/cocohet.Rd
Log:
prepare to patch bug [#2672] (GenABEL::cocohet default graph output) - documentation converted to roxygen, code re-styled
Modified: pkg/GenABEL/R/cocohet.R
===================================================================
--- pkg/GenABEL/R/cocohet.R 2013-04-04 11:46:15 UTC (rev 1187)
+++ pkg/GenABEL/R/cocohet.R 2013-04-09 15:17:56 UTC (rev 1188)
@@ -1,197 +1,225 @@
-#=====================================================================================
-#
-# Filename: chi2-CG.R
-#
-# Description: Functions for performing chi2 test for Detecting Rare Recessive Alleles.
-#
-# Version: 1.0
-# Created: 27-May-2010
-# Revision: none
-#
-#
-# Author: Maksim V. Struchalin
-# Company: ErasmusMC, Epidemiology, The Netherlands.
-# Email: m.struchalin at erasmusmc.nl
-#
-#=====================================================================================
-
-
-"cocohet" <- function(data, trait, window, return_all_result=TRUE, manhettan_filename="manhettan_plot.jpeg", test="CHI2", min_expected_cut_off=-1)
+#' Detecting rare recessive and compound heterozygote alleles in genome wide
+#' association.
+#'
+#' The function is an inplementation of the method aimed to detect a
+#' gene-phenotype association caused by recessive and compound heterozygote
+#' genotype states of multiple rare variants at a particular gene locus. This
+#' method is described in 'Detecting Low Frequent Loss-of-Function Alleles in
+#' Genome Wide Association Studies with Red Hair Color as Example'; Fan Liu,
+#' Maksim V. Struchalin, Kate van Duijn, Albert Hofman, Andre G. Uitterlinden,
+#' Yurii S. Aulchenko, and Manfred Kayser. PLoS ONE 6(11): e28145.
+#' doi:10.1371/journal.pone.0028145
+#'
+#' The three tests are implemented: Pearson's chi-square test, Pearson's
+#' chi-square test with Yates correction, Fisher exact test. In case when the
+#' input parameter min_expected_cut_off is <0 the choosen in the input
+#' parameter "test" test is performed. If min_expected_cut_off >= 0 then always
+#' Pearson's chi-square test is performed exept of the cases when expected
+#' number of subjects in a field of contingency table is <min_expected_cut_off.
+#' In this case the test choosen in the input parameter test is performed.
+#'
+#' @aliases cocohet chi2_CG
+#' @param data Genotype data for analysis. Object of class
+#' \code{\link{snp.data}}
+#' @param trait Vector with binary trait data. Object of class
+#' \code{\link{integer}} or \code{\link{numeric}}.
+#' @param window Number of SNPs on the "right" of a given SNP which are used in
+#' analysis with a SNP. Object of class \code{\link{integer}}
+#' @param return_all_result If FALSE then return only a vector where each
+#' element is a chisq obtained as a maximum chisq between a given SNP and SNPs
+#' on the right within a window. If TRUE then return also a matrix where
+#' chisq's for all tests are stored. Object of class \code{\link{logical}}
+#' @param manhettan_filename File name where manhettan plot will be saved after
+#' analysis. Object of class \code{\link{character}}
+#' @param test Name of the test to be performed. Available tests are "CHI2",
+#' "YATES" (chi2 with Yates correction), and "FISHER". Object of class
+#' \code{\link{character}}
+#' @param min_expected_cut_off In case this is >=0 and test is NOT Pearson's
+#' chisq test then Pearson's chisq test (!) is performed only for SNPs which
+#' produce acontingency table where the expected number of subjects in each
+#' field is >min_expected_cut_off. Otherwise the specified test is performed.
+#' Object of class \code{\link{integer}} or \code{\link{numeric}}
+#' @return A list is returned.
+#' @returnItem chi2_max A vector where each element is a test statistic choosen
+#' as a maximum chisq among tests where a SNP and SNPs on the right within a
+#' window are involved.
+#' @returnItem chi2_all Statistics of all tests done in the analysis. Each row
+#' of the matrix contains tests statistics for a SNP and all SNPs on the right
+#' of him within of a given window. For example: the ellement chi2_all[1,1]
+#' stands for a test
+#' @references
+#' Fan Liu, Maksim V. Struchalin, Kate van Duijn, Albert Hofman, Andre G.
+#' Uitterlinden, Yurii S. Aulchenko, and Manfred Kayser. Detecting Low
+#' Frequent Loss-of-Function Alleles in Genome Wide Association Studies
+#' with Red Hair Color as Example'. PLoS ONE 6(11): e28145.
+#' doi:10.1371/journal.pone.0028145
+#' @author Maksim Struchalin
+#' @keywords manip
+#' @examples
+#' data(srdta)
+#' chis2_nocorrection <- cocohet(data=srdta at gtdata, trait=srdta at phdata$bt, window=3, test="CHI2")
+#'
+"cocohet" <- function(data, trait, window, return_all_result=TRUE,
+ manhettan_filename="manhettan_plot.jpeg", test="CHI2",
+ min_expected_cut_off=-1)
{
#Correction is performed in case expected value one of the margin in contigency table less 5. Available values for chi2_correction:
# "CHI2"
# "YATES"
# "FISHER"
+ if(!is(data, "snp.data")) {
+ stop("Wrong data class: the argument \"data\" should has type \"snp.data\".")
+ }
+
+ if(!is(trait, "integer") && !is(trait, "numeric")) {
+ stop("Wrong data class: the argument \"trait\" should has type \"integer\" or \"numeric\".")
+ }
+
+ if(dim(table(trait)) != 2) {
+ stop("\"trait\" must be binary")
+ }
+ if(!is(window, "integer") && !is(window, "numeric")) {
+ stop("Wrong data class: the argument \"window\" should has type \"integer\" or \"numeric\".")
+ }
+
+ snp_number <- data at nsnps
-if(!is(data,"snp.data"))
- {
- stop("Wrong data class: the argument \"data\" should has type \"snp.data\".")
- }
+ if(window >= snp_number) {
+ print(paste("warning: \"window\" value ", window, " is bigger than total snp number. Automaticly reduced to maximum possible."))
+ window <- snp_number - 1
+ print(paste("New window value is ", window, ".\n"))
+ }
+ if(window==0) {stop("Input parameter window can not be zero.\n")}
+ output <- .Call("interaction_rare_recesive_allele_C_", as.raw(data at gtps), as.integer(data at nids), as.integer(snp_number),
+ as.integer(trait),
+ as.integer(window),
+ return_all_result,
+ test,
+ as.integer(min_expected_cut_off))
+ results <- list()
+ results$chi2_max <- output[1:(data at nsnps-1)]
+ if(return_all_result) {
+ results$chi2_all <- matrix(output[data at nsnps:length(output)], ncol=window, nrow=data at nsnps-1, byrow=T)
+ }
-if(!is(trait, "integer") && !is(trait, "numeric"))
- {
- stop("Wrong data class: the argument \"trait\" should has type \"integer\" or \"numeric\".")
- }
-
-if(dim(table(trait)) != 2)
- {
- stop("\"trait\" must be binary")
- }
-
-
-if(!is(window, "integer") && !is(window, "numeric"))
- {
- stop("Wrong data class: the argument \"window\" should has type \"integer\" or \"numeric\".")
- }
-
-
-
-snp_number <- data at nsnps
-
-
-if(window >= snp_number)
- {
- print(paste("warning: \"window\" value ", window, " is bigger than total snp number. Automaticly reduced to maximum possible."))
- window <- snp_number - 1
- print(paste("New window value is ", window, ".\n"))
- }
-
-if(window==0) {stop("Input parameter window can not be zero.\n")}
-
-
-
-output <- .Call("interaction_rare_recesive_allele_C_", as.raw(data at gtps), as.integer(data at nids), as.integer(snp_number),
- as.integer(trait),
- as.integer(window),
- return_all_result,
- test,
- as.integer(min_expected_cut_off))
-
-
-
-results <- list()
-
-results$chi2_max <- output[1:(data at nsnps-1)]
-if(return_all_result)
- {
- results$chi2_all <- matrix(output[data at nsnps:length(output)], ncol=window, nrow=data at nsnps-1, byrow=T)
- }
-
-
-
-print("plotting manhettan plot picture...")
-bitmap(manhettan_filename, type="jpeg")
-results_pval <- pchisq(results$chi2_max, df=1, lower.tail=F)
-results_list <- list()
-results_list$P1df <- results_pval
-results_list$map <- data at map[1:(data at nsnps-1)]
-results_list$chromosome <- data at chromosome[1:(data at nsnps-1)]
-class(results_list) <- "scan.gwaa"
-print("1")
-try(plot.scan.gwaa(results_list))
-print("2")
-dev.off()
-print(paste("The plot is saved into file ", manhettan_filename, sep=""))
-
-
-
-snp_position_top <- which.max(results$chi2_max)
-snp_name_top <- data at snpnames[snp_position_top]
-snp_chromosome_top <- data at chromosome[snp_position_top]
-snp_map_top <- data at map[snp_position_top]
-
-print(paste("The top snp has name ", snp_name_top, ",is located in chromosome ", snp_chromosome_top, ", position ", snp_map_top, sep=""))
-
+ print("plotting manhettan plot picture...")
+ bitmap(manhettan_filename, type="jpeg")
+ results_pval <- pchisq(results$chi2_max, df=1, lower.tail=F)
+ results_list <- list()
+ results_list$P1df <- results_pval
+ results_list$map <- data at map[1:(data at nsnps-1)]
+ results_list$chromosome <- data at chromosome[1:(data at nsnps-1)]
+ class(results_list) <- "scan.gwaa"
+ print("1")
+ try(plot.scan.gwaa(results_list))
+ print("2")
+ dev.off()
+ print(paste("The plot is saved into file ", manhettan_filename, sep=""))
+
+ snp_position_top <- which.max(results$chi2_max)
+ snp_name_top <- data at snpnames[snp_position_top]
+ snp_chromosome_top <- data at chromosome[snp_position_top]
+ snp_map_top <- data at map[snp_position_top]
+
+ print(paste("The top snp has name ", snp_name_top, ",is located in chromosome ", snp_chromosome_top, ", position ", snp_map_top, sep=""))
+
#if(return_all_result)
# {
# print(paste("Plotting the manhettan plot for interaction bewteen snp ", snp_name_top, " and snps on the left/right within a window", sep=""))
# look_at_snp_chi2s_interactions_rare_recesive_alleles(results$chi2_all, data, snp_position_top)
# }
-
-results
+
+ results
}
-
-
-
-
-
-"look_at_snp_chi2s_interactions_rare_recesive_alleles" <- function(chi2_all, data, snp_position, manhettan_filename="one_snp_manhettan.jpeg")
+#TODO it seems the function below is never used - should it be deleted from the code?
+"look_at_snp_chi2s_interactions_rare_recesive_alleles" <- function(
+ chi2_all, data, snp_position,
+ manhettan_filename="one_snp_manhettan.jpeg")
{
-if(!is(data,"snp.data"))
- {
- stop("Wrong data class: the argument \"data\" should has type \"snp.data\".")
- }
-
-
-if(!is(chi2_all,"matrix"))
- {
- stop("Wrong data class: the argument \"chi2_all\" should has type \"matrix\".")
- }
-
-
-
-
-window <- dim(chi2_all)[2]
-snp_number <- dim(chi2_all)[1] + 1
-
-if(window == 0 | snp_number==0) stop("Wrong chi2 matrix.")
-
-results <- list()
-results$right_window_chi2s <- chi2_all[snp_position,]
-results$left_window_chi2s <- c()
-
-left_border <- snp_position - window
-if(left_border <=0 ) left_border <- 1
-
-right_border <- snp_position + window
-if(right_border > snp_number-1) right_border <- snp_number-1
-
-for(i in 1:left_border)
- {
- results$left_window_chi2s <- c(results$left_window_chi2s, chi2_all[snp_position-i, i])
- }
-
-bitmap(manhettan_filename, type="jpeg")
-
-print(snp_position)
-results_chi2 <- c(results$left_window_chi2s, results$right_window_chi2s)
-print(length(results$left_window_chi2s))
-print(length(results$right_window_chi2s))
-print(length(results_chi2))
-print("________________")
-results_pval <- pchisq(results_chi2, df=1, lower.tail=F)
-
-max_position_local <- which.max(results_chi2)
-max_position <- max_position_local + snp_position
-
-results_list <- list()
-results_list$P1df <- results_pval
-results_list$map <- c(data at map[left_border:(snp_position-1)], data at map[(snp_position+1):right_border])
-results_list$chromosome <- as.factor(c(as.character(data at chromosome[left_border:(snp_position-1)]),
- as.character(data at chromosome[(snp_position+1):right_border])))
-class(results_list) <- "scan.gwaa"
-
-
-print(length(results_list$P1df))
-print(length(results_list$map))
-print(length(results_list$chromosome))
-
-try(plot.scan.gwaa(results_list))
-
-dev.off()
-
-print(paste("The plot is saved into file ", manhettan_filename, sep=""))
-
-print(paste("Maximum chi2 is ", results_chi2[max_position_local], " for a snp in position ", max_position, sep=""))
-
-
-results_chi2
+ if(!is(data,"snp.data")) {
+ stop("Wrong data class: the argument \"data\" should has type \"snp.data\".")
+ }
+
+ if(!is(chi2_all,"matrix")) {
+ stop("Wrong data class: the argument \"chi2_all\" should has type \"matrix\".")
+ }
+
+ window <- dim(chi2_all)[2]
+ snp_number <- dim(chi2_all)[1] + 1
+
+ if(window == 0 | snp_number==0) stop("Wrong chi2 matrix.")
+
+ results <- list()
+ results$right_window_chi2s <- chi2_all[snp_position,]
+ results$left_window_chi2s <- c()
+
+ left_border <- snp_position - window
+ if(left_border <=0 ) left_border <- 1
+
+ right_border <- snp_position + window
+ if(right_border > snp_number-1) right_border <- snp_number-1
+
+ for(i in 1:left_border)
+ {
+ results$left_window_chi2s <- c(results$left_window_chi2s, chi2_all[snp_position-i, i])
+ }
+
+ bitmap(manhettan_filename, type="jpeg")
+
+ print(snp_position)
+ results_chi2 <- c(results$left_window_chi2s, results$right_window_chi2s)
+ print(length(results$left_window_chi2s))
+ print(length(results$right_window_chi2s))
+ print(length(results_chi2))
+ print("________________")
+ results_pval <- pchisq(results_chi2, df=1, lower.tail=F)
+
+ max_position_local <- which.max(results_chi2)
+ max_position <- max_position_local + snp_position
+
+ results_list <- list()
+ results_list$P1df <- results_pval
+ results_list$map <- c(data at map[left_border:(snp_position-1)], data at map[(snp_position+1):right_border])
+ results_list$chromosome <- as.factor(c(as.character(data at chromosome[left_border:(snp_position-1)]),
+ as.character(data at chromosome[(snp_position+1):right_border])))
+ class(results_list) <- "scan.gwaa"
+
+
+ print(length(results_list$P1df))
+ print(length(results_list$map))
+ print(length(results_list$chromosome))
+
+ try(plot.scan.gwaa(results_list))
+
+ dev.off()
+
+ print(paste("The plot is saved into file ", manhettan_filename, sep=""))
+
+ print(paste("Maximum chi2 is ", results_chi2[max_position_local], " for a snp in position ", max_position, sep=""))
+
+
+ results_chi2
}
-
-
+# original header moved here because the roxygen doc is not at the beginning
+#=====================================================================================
+#
+# Filename: chi2-CG.R
+#
+# Description: Functions for performing chi2 test for Detecting Rare Recessive Alleles.
+#
+# Version: 1.0
+# Created: 27-May-2010
+# Revision: none
+#
+#
+# Author: Maksim V. Struchalin
+# Company: ErasmusMC, Epidemiology, The Netherlands.
+# Email: m.struchalin at erasmusmc.nl
+#
+#=====================================================================================
Modified: pkg/GenABEL/generate_documentation.R
===================================================================
--- pkg/GenABEL/generate_documentation.R 2013-04-04 11:46:15 UTC (rev 1187)
+++ pkg/GenABEL/generate_documentation.R 2013-04-09 15:17:56 UTC (rev 1188)
@@ -1,40 +1,41 @@
roxy_files <- c(
- "add.phdata.R",
- #"annotation",
- "arrange_probabel_phe.R",
- "blurGenotype.R",
- "checkPackageVersionOnCRAN.R",
- "del.phdata.R",
- "egscore.R",
- "estlambda.R",
- "export.plink.R",
- "extract.annotation.impute.R",
- "extract.annotation.mach.R",
- "findRelatives.R",
- "GC.R",
- "GC_ovdom.R",
- "GenABEL.R",
- "generateOffspring.R",
- "getLogLikelihoodGivenRelation.R",
- "grammar.R",
- "hom.R",
- "ibs.R",
- "impute2databel.R",
- "impute2mach.R",
- #"LiLogCC.R",
- #"LiLog.R",
- "mach2databel.R",
- "makeTransitionMatrix.R",
- #"phdata.R",
- "PGC.R",
- "polygenic.R",
- "polygenic_hglm.R",
- "qtscore.R",
- "recodeChromosome.R",
- "reconstructNPs.R",
- "sortmap.internal.R"
- #,
- #"summary.scan.gwaa.R"
+ "add.phdata.R",
+ #"annotation",
+ "arrange_probabel_phe.R",
+ "blurGenotype.R",
+ "checkPackageVersionOnCRAN.R",
+ "cocohet.R",
+ "del.phdata.R",
+ "egscore.R",
+ "estlambda.R",
+ "export.plink.R",
+ "extract.annotation.impute.R",
+ "extract.annotation.mach.R",
+ "findRelatives.R",
+ "GC.R",
+ "GC_ovdom.R",
+ "GenABEL.R",
+ "generateOffspring.R",
+ "getLogLikelihoodGivenRelation.R",
+ "grammar.R",
+ "hom.R",
+ "ibs.R",
+ "impute2databel.R",
+ "impute2mach.R",
+ #"LiLogCC.R",
+ #"LiLog.R",
+ "mach2databel.R",
+ "makeTransitionMatrix.R",
+ #"phdata.R",
+ "PGC.R",
+ "polygenic.R",
+ "polygenic_hglm.R",
+ "qtscore.R",
+ "recodeChromosome.R",
+ "reconstructNPs.R",
+ "sortmap.internal.R"
+#,
+#"summary.scan.gwaa.R"
)
library(roxygen2)
Modified: pkg/GenABEL/man/cocohet.Rd
===================================================================
--- pkg/GenABEL/man/cocohet.Rd 2013-04-04 11:46:15 UTC (rev 1187)
+++ pkg/GenABEL/man/cocohet.Rd 2013-04-09 15:17:56 UTC (rev 1188)
@@ -1,59 +1,88 @@
\name{cocohet}
+\alias{chi2_CG}
\alias{cocohet}
-\alias{chi2_CG}
-\title{Detecting rare recessive and compound heterozygote alleles in genome wide association.}
-\description{
-Detecting rare recessive and compound heterozygote alleles in genome wide association.
-}
+\title{Detecting rare recessive and compound heterozygote alleles in genome wide
+association.}
\usage{
-cocohet(data, trait, window, return_all_result=TRUE, manhettan_filename="manhettan_plot.jpeg", test="CHI2", min_expected_cut_off=-1)
+ cocohet(data, trait, window, return_all_result = TRUE,
+ manhettan_filename = "manhettan_plot.jpeg",
+ test = "CHI2", min_expected_cut_off = -1)
}
\arguments{
- \item{data}{Genotype data for analysis. Object of class \code{\link{snp.data}}}
- \item{trait}{Vector with binary trait data. Object of class \code{\link{integer}} or \code{\link{numeric}}.}
- \item{window}{Number of SNPs on the "right" of a given SNP which are used in analysis with a SNP. Object of class \code{\link{integer}}}
- \item{return_all_result}{If FALSE then return only a vector where each element is a chisq obtained as a maximum chisq between a given SNP and SNPs on the right within a window. If TRUE then return also a matrix where chisq's for all tests are stored. Object of class \code{\link{logical}}}
- \item{manhettan_filename}{File name where manhettan plot will be saved after analysis. Object of class \code{\link{character}}}
- \item{test}{Name of the test to be performed. Available tests are "CHI2", "YATES" (chi2 with Yates correction), and "FISHER". Object of class \code{\link{character}}}
- \item{min_expected_cut_off}{In case this is >=0 and test is NOT Pearson's chisq test then Pearson's chisq test (!) is performed only for SNPs which produce acontingency table where the expected number of subjects in each field is >min_expected_cut_off. Otherwise the specified test is performed. Object of class \code{\link{integer}} or \code{\link{numeric}}}
-}
-\details{
+ \item{data}{Genotype data for analysis. Object of class
+ \code{\link{snp.data}}}
-The function is an inplementation of the method aimed to detect a
-gene-phenotype association caused by recessive and compound heterozygote
-genotype states of multiple rare variants at a particular gene
-locus. This method is described in 'Detecting Low Frequent
-Loss-of-Function Alleles in Genome Wide Association Studies with Red
-Hair Color as Example'; Fan Liu, Maksim V. Struchalin, Kate van Duijn,
-Albert Hofman, Andre G. Uitterlinden, Yurii S. Aulchenko, and Manfred
-Kayser. PLoS ONE 6(11): e28145. doi:10.1371/journal.pone.0028145
+ \item{trait}{Vector with binary trait data. Object of
+ class \code{\link{integer}} or \code{\link{numeric}}.}
+ \item{window}{Number of SNPs on the "right" of a given
+ SNP which are used in analysis with a SNP. Object of
+ class \code{\link{integer}}}
-The three tests are implemented: Pearson's chi-square test, Pearson's chi-square test with Yates correction, Fisher exact test.
-In case when the input parameter min_expected_cut_off is <0 the choosen in the input parameter "test" test is performed. If min_expected_cut_off >= 0
-then always Pearson's chi-square test is
-performed exept of the cases when expected number of subjects in a field of contingency table is <min_expected_cut_off. In this case the test choosen in
-the input parameter test is performed.
+ \item{return_all_result}{If FALSE then return only a
+ vector where each element is a chisq obtained as a
+ maximum chisq between a given SNP and SNPs on the right
+ within a window. If TRUE then return also a matrix where
+ chisq's for all tests are stored. Object of class
+ \code{\link{logical}}}
+ \item{manhettan_filename}{File name where manhettan plot
+ will be saved after analysis. Object of class
+ \code{\link{character}}}
+ \item{test}{Name of the test to be performed. Available
+ tests are "CHI2", "YATES" (chi2 with Yates correction),
+ and "FISHER". Object of class \code{\link{character}}}
+
+ \item{min_expected_cut_off}{In case this is >=0 and test
+ is NOT Pearson's chisq test then Pearson's chisq test (!)
+ is performed only for SNPs which produce acontingency
+ table where the expected number of subjects in each field
+ is >min_expected_cut_off. Otherwise the specified test is
+ performed. Object of class \code{\link{integer}} or
+ \code{\link{numeric}}}
}
\value{
- A list is returned.
- \item{chi2_max}{A vector where each element is a test statistic choosen as a maximum chisq among tests where a SNP and SNPs on the right within a window are involved.}
- \item{chi2_all}{Statistics of all tests done in the analysis. Each row of the matrix contains tests statistics for a SNP and all SNPs on the right of him within of a given window.
- For example: the ellement chi2_all[1,1] stands for a test }
+ A list is returned.
}
-%\references{ ~put references to the literature/web site here ~ }
-\author{Maksim Struchalin}
-%\note{ ~~further notes~~
-%}
-
+\description{
+ The function is an inplementation of the method aimed to
+ detect a gene-phenotype association caused by recessive
+ and compound heterozygote genotype states of multiple
+ rare variants at a particular gene locus. This method is
+ described in 'Detecting Low Frequent Loss-of-Function
+ Alleles in Genome Wide Association Studies with Red Hair
+ Color as Example'; Fan Liu, Maksim V. Struchalin, Kate
+ van Duijn, Albert Hofman, Andre G. Uitterlinden, Yurii S.
+ Aulchenko, and Manfred Kayser. PLoS ONE 6(11): e28145.
+ doi:10.1371/journal.pone.0028145
+}
+\details{
+ The three tests are implemented: Pearson's chi-square
+ test, Pearson's chi-square test with Yates correction,
+ Fisher exact test. In case when the input parameter
+ min_expected_cut_off is <0 the choosen in the input
+ parameter "test" test is performed. If
+ min_expected_cut_off >= 0 then always Pearson's
+ chi-square test is performed exept of the cases when
+ expected number of subjects in a field of contingency
+ table is <min_expected_cut_off. In this case the test
+ choosen in the input parameter test is performed.
+}
\examples{
-
data(srdta)
-chis2_nocorrection <- cocohet(data=srdta at gtdata, trait=srdta at phdata$bt, window=3, test="CHI2")
-
+chis2_nocorrection <- cocohet(data=srdta
}
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
+\author{
+ Maksim Struchalin
+}
+\references{
+ Fan Liu, Maksim V. Struchalin, Kate van Duijn, Albert
+ Hofman, Andre G. Uitterlinden, Yurii S. Aulchenko, and
+ Manfred Kayser. Detecting Low Frequent Loss-of-Function
+ Alleles in Genome Wide Association Studies with Red Hair
+ Color as Example'. PLoS ONE 6(11): e28145.
+ doi:10.1371/journal.pone.0028145
+}
\keyword{manip}
+
More information about the Genabel-commits
mailing list