R/haplo.em.control.q

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

#$Author: sinnwell $
#$Date: 2008/02/05 16:31:18 $
#$Header: /projects/genetics/cvs/cvsroot/haplo.stats/R/haplo.em.control.q,v 1.7 2008/02/05 16:31:18 sinnwell Exp $
#$Locker:  $
#$Log: haplo.em.control.q,v $
#Revision 1.7  2008/02/05 16:31:18  sinnwell
#change default for min.posteror to 1e-9 for when all lowLD markers, sometimes a subject is completely removed.
#
#Revision 1.6  2007/10/16 19:08:30  sinnwell
#put max.haps.limit back in, and make the max allowed by intMax by checkIntMax in C, set limit at 2e6 as that seemed to work in previous versions
#
#Revision 1.5  2007/02/27 20:14:03  schaid
#removed max.haps.limit, which is now controlled by checkIntMax in haplo.em and in haplol_em_pin
#
#Revision 1.4  2005/03/02 15:12:31  schaid
#changed max.iter to 5000
#
#Revision 1.3  2003/11/17 23:28:10  schaid
#made compatible with R
#
#Revision 1.2  2003/08/26 22:09:38  sinnwell
#added GPL License
#
#Revision 1.1  2003/08/26 21:02:09  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
# 
haplo.em.control <- function(loci.insert.order=NULL,
                             insert.batch.size = 6,
                             min.posterior=1e-9,
                             tol=0.00001,
                             max.iter=5000,
                             random.start=0,
                             n.try = 10,
                             iseed=NULL,
                             max.haps.limit = 2e6,
                             verbose=0) {


  if(min.posterior < 0 | min.posterior > .8) {
    warning("The value of min.posterior is out of range, the devault value of 1e-9 is used instead")
    min.posterior <-  1e-9
  }

  if(tol < 0 | tol > .5) {
    warning("The value of tol is out of range, the default value of 0.00001 is used instead")
    tol <- 0.00001
  }


  if(max.iter < 0) { 
    warning("The value of max.iter is < 0, the default value of 5000 is used instead")
    max.iter <- 5000
  }

  if(random.start !=0  & random.start != 1){
    warning("The value of random.start is not valid, the default value of 0 is used instead")
    random.start <- 0
  }

  if(n.try < 1){
    warning("The value of n.try is not valid, the default value of 10 is used instead")
    n.try <- 10
  }

  # max.haps.limit is used to allow user to specify max number of hap pairs.
  # -If run-time is an issue with a small data set, set to a low number
  # -If set too-low for number of haplotypes, the C functions must request more, which takes extra time
  
  # Employ the system's intMax as the upper limit allowed by integer index (int representation in R)
  # In most situations, the process is unable to allocate memory for intMax,
  # which is roughly 5-6G of total memory in haplo.em test cases
  intMax <- .C("checkIntMax",
               intMax = as.integer(0),
               PACKAGE="haplo.stats")$intMax
  
  if(max.haps.limit < 1000 | max.haps.limit > intMax) {
    warning("The value of max.haps.limit is not valid, the default value of 2e6 is used instead")
    max.haps.limit = 2e6
  }

  
  return(list(loci.insert.order=loci.insert.order, 
              insert.batch.size = insert.batch.size,
              min.posterior=min.posterior, 
              tol=tol, 
              max.iter=max.iter, 
              random.start=random.start,
              n.try=n.try,
              iseed=iseed,
              max.haps.limit=max.haps.limit,
              verbose=verbose))
}