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#' delete phenotypes from phdata
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#' This function is used to delete certain
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#' phenotypes from phenotypic part (phdata)
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#' of an object of \code{\link{gwaa.data-class}}
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#' @param data an object of \code{\link{gwaa.data-class}}
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#' @param what which phenotypes (variables) to delete, expressed
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#' as (vector of) names (character) or integer (column of
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#' @param all if 'all'=TRUE and 'what' is misisng,
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#' all phenotypes are deleted, and only the 'id'
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#' @author Yurii Aulchenko
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#' phdata(srdta)[1:5,]
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#' srdta <- del.phdata(srdta,"qt1")
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#' phdata(srdta)[1:5,]
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#' srdta <- del.phdata(srdta,all=TRUE)
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#' phdata(srdta)[1:5,]
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del.phdata <- function(data,what,all=FALSE)
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if (class(data) != "gwaa.data") stop("data should be of gwaa.data-class");
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if (missing(what) && all) {
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cat("Deleting all data but 'id' and 'sex'\n")
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data@phdata <- data@phdata[,c("id","sex")]
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if (missing(what)) stop("'what' could be missing only if 'all'=TRUE (delete all data)")
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if (is.integer(what)) what <- names(data@phdata)[what]
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if (any(what == "id")) stop("you can not delete 'id'")
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if (any(what == "sex")) stop("you can not delete 'sex'")
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nms <- names(data@phdata);
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tokeep <- nms[!(nms %in% what)];
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data@phdata <- data@phdata[,tokeep]
b'\\ No newline at end of file'
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R/del.phdata.R
