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#$Author: sinnwell $
#$Date: 2006/11/09 22:23:10 $
#$Header: /people/biostat3/sinnwell/Projects/IBDReg/Make/RCS/plot.ibdreg.unexpect.q,v 1.1 2006/11/09 22:23:10 sinnwell Exp $
#$Locker: $
#$Log: plot.ibdreg.unexpect.q,v $
#Revision 1.1 2006/11/09 22:23:10 sinnwell
#Initial revision
#
#Revision 1.1 2006/05/19 18:12:15 sinnwell
#Initial revision
#
##################################
# Jason Sinnwell
# Daniel Schaid
# Mayo Clinic, HSR, Biostatistics
# ibdreg package 2006
##################################
plot.ibdreg.unexpect <- function(x, status.method="AA", ...) {
if(!inherits(x, "ibdreg"))
stop("Not an ibdreg object")
tests.obj <- switch(status.method,
"AA" = x$AA.linkage,
"AU" = x$AU.linkage,
"UU" = x$UU.linkage,
stop("status method not understood"))
xpos <- tests.obj$linkage.frame$positions
linkage.only <- tests.obj$ncov==1
# pull off title parm from ellipsis, eg. an extra label for chrom, etc
dots <- as.list(substitute(list(...)))[-1]
title.indx <- match('title', names(dots))
title.user <- if(!is.na(title.indx)) dots[title.indx]$title else NULL
minp <- min(c(.001, # corresponds to upper ylim=3
tests.obj$linkage.cons.frame$pval.linkage.cons,
tests.obj$linkage.frame$pval.linkage))
plotpval(pos=xpos, pmat=cbind(tests.obj$linkage.cons.frame$pval.linkage.cons,
tests.obj$linkage.frame$pval.linkage),
lty=c(1,2), col=c(1,2), lwd=c(2,2),
title=paste(title.user, "\n", tests.obj$status.method,
"PAIRS: Constrained versus Unconstrained Linkage", sep=" "),
legend=c("Constrained", "Unconstrained"))
invisible(x)
}
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