R/summary.haplo.em.q

In haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

#$Author: sinnwell $
#$Date: 2008/11/25 22:11:00 $
#$Header: /projects/genetics/cvs/cvsroot/haplo.stats/R/summary.haplo.em.q,v 1.9 2008/11/25 22:11:00 sinnwell Exp $
#$Locker:  $
#$Log: summary.haplo.em.q,v $
#Revision 1.9  2008/11/25 22:11:00  sinnwell
#return table of haps by invisible
#
#Revision 1.8  2007/11/07 21:33:37  sinnwell
#add digits
#
#Revision 1.7  2004/04/06 20:40:00  sinnwell
#use nlines to limit lines in vignettes
#
#Revision 1.6  2004/02/26 23:10:39  sinnwell
#print.banner to printBanner
#
#Revision 1.5  2004/02/16 19:41:01  sinnwell
#add '...' to make method for haplo.em object
#
#Revision 1.4  2003/12/08 20:24:09  sinnwell
# changed T,F to TRUE,FALSE
#
#Revision 1.3  2003/10/15 15:41:18  schaid
#added show.haplo option for showing haplotypes instead of their codes
#
#Revision 1.2  2003/08/26 22:09:38  sinnwell
#added GPL License
#
#Revision 1.1  2003/08/26 21:00:25  schaid
#Initial revision
#
# License: 
# 
# Copyright 2003 Mayo Foundation for Medical Education and Research. 
# 
# This program is free software; you can redistribute it and/or modify it under the terms of 
# the GNU General Public License as published by the Free Software Foundation; either 
# version 2 of the License, or (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful, but WITHOUT ANY 
# WARRANTY; without even the implied warranty of MERCHANTABILITY or 
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for 
# more details.
# 
# You should have received a copy of the GNU General Public License along with this 
# program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, 
# Boston, MA 02111-1307 USA
# 
# For other licensing arrangements, please contact Daniel J. Schaid.
# 
# Daniel J. Schaid, Ph.D.
# Division of Biostatistics
# Harwick Building Room 775
# Mayo Clinic
# 200 First St., SW
# Rochester, MN 55905
# 
# phone: 507-284-0639
# fax:      507-284-9542
# email: schaid@mayo.edu
# 
summary.haplo.em <- function(object, show.haplo=FALSE,
                             digits=max(options()$digits-2, 5), nlines=NULL, ...){
  
  printBanner("Subjects: Haplotype Codes and Posterior Probabilities")
  hap1sorted <- ifelse(object$hap1code < object$hap2code, object$hap1code, object$hap2code)
  hap2sorted <- ifelse(object$hap1code < object$hap2code, object$hap2code, object$hap1code)
  if(show.haplo){    
     hap1 <- object$haplotype[object$hap1code,]
     hap2 <- object$haplotype[object$hap2code,]
     
     df <- data.frame(subj.id=object$subj.id, hap1=object$haplotype[hap1sorted,], hap2=object$haplotype[hap2sorted,],
                      ##hap1=hap1, hap2=hap2,
                    posterior=round(object$post,digits))
  }  else{
     df <- data.frame(subj.id=object$subj.id, hap1=hap1sorted, hap2=hap2sorted,
                      #hap1code=object$hap1code, hap2code=object$hap2code,
                    posterior=round(object$post, digits))
  }
  df <- df[order(max(df$subj.id)-df$subj.id, df$posterior, decreasing=TRUE),]
  rownames(df) <- 1:nrow(df)
  if(is.null(nlines)) print(df)
  else print(df[1:nlines,])
  
  printBanner("Number of haplotype pairs: max vs used")
 

  x <- object$max.pairs
  if(length(object$rows.rem) > 0 ){
    x <- x[-object$rows.rem]
  } 
  print(table(x, object$nreps))

  invisible(df)
}