generate_documentation.R

roxy_files <- c(
        "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",
        "VIFGC.R",
        "VIFGC_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)
setwd("R")
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)
unlink("GenABEL",recursive=TRUE)