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#####################################################################
#
# cleanphe.R
#
# copyright (c) 2008-3, Ahmid A Khalili
#
# last modified Jul, 2008
# first written Mar, 2008
# Licensed under the GNU General Public License version 2 (June, 1991)
#
# Part of the R/eqtl package
# Contains: cleanphe
#
######################################################################
######################################################################
#
# cleanphe: Remove undesired phenotypes and LOD results from cross
# and scanone object respectively
#
######################################################################
`cleanphe` <-
function(x,string='Buffer')
{
require(qtl)
if ( ! any(class(x) == 'cross') & ! any(class(x) == 'scanone') )
stop("Input should have class \"cross\" or class \"scanone\".")
if ( ! is.character(string) & !is.vector(string))
stop("Expecting a characte r vector for string")
if ( class(x)[1] == 'scanone') {
coord <- grep(string,names(x))
cat("Drop ",length(coord),"lodcolumn\n");
if(!length(coord)) return(x);
nf <- x[,-coord]
} else {
coord <- grep(string,names(x$pheno))
cat("Drop ",length(coord),"phenotypes\n");
if(!length(coord)) return(x);
nf <- x
nf$pheno <- x$pheno[,-coord]
}
attributes(nf)$class <- class(x)
try(return(nf),silent=FALSE)
}
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