version 1.0-1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bqtl
-Version: 1.0
-Date: 2001-02-28
+Version: 1.0-1
+Date: 2001-03-09
 Title: Bayesian QTL mapping toolkit 
 Author: Charles C. Berry <cberry@ucsd.edu>
 Maintainer: Charles C. Berry <cberry@ucsd.edu>

R/make.map.frame.s

@@ -105,7 +105,8 @@
     locus<-paste("C",chr.num,as.numeric(format(100*mgd/morgan,digits=4)),
                  sep=".")
     res <- data.frame(
-                      marker.name=as.character(make.names(marker.names,TRUE)),
+                      marker.name=
+                      I(as.character(make.names(marker.names,TRUE))),
                       cM=as.numeric(mgd),
                       prior=as.numeric(prior),
                       pos.type=I(pos.type),

man/a.starting.point.for.bqtl.Rd

@@ -1,5 +1,5 @@
 \name{A Starting Point}
-
+\alias{A Starting Point}
 \title{Some Introductory Comments}
 \description{Some pointers to a few key functions in \emph{BQTL}}
 
@@ -24,38 +24,39 @@
 }
 \section{Key Functions}{
   \describe{
-    \item{Data Input}{ }
-
+    \item{Data Input}{ \  }
+    
       \describe{
-	\item{\code{make.map.frame}}{defines the map,}
+	\item{\code{\link{make.map.frame}}}{defines the map,}
 
-	\item{\code{marker.levels}}{defines the coding scheme for
+	\item{\code{\link{marker.levels}}}{The help page describes several
+	  functions that define the coding scheme for
 	  marker levels, }
 
-	\item{\code{make.analysis.obj}}{combines marker data, phenotype
+	\item{\code{\link{make.analysis.obj}}}{combines marker data, phenotype
 	  data,and the \code{map.frame} to create an object that can be
 	  used by data analysis functions.}
 
       }
-
-      \item{Maximum Likelihood Methods}{ }
+      \item{Maximum Likelihood Methods}{ \  }
 
       \describe{
-       \item{\code{bqtl}}{does a host of things from marker regression
+       \item{\code{\link{bqtl}}}{does a host of things from marker regression
 	 and interval mapping to full maximum likelihood. The best way to
 	 get started is to run \code{example(bqtl)} and take a look at
 	 the resulting output.}
 
-       \item{\code{locus}}{ is very helpful in specification of runs.} 
+       \item{\code{\link{locus}}}{ is very helpful in specification of runs.} 
      }
 
-     \item{Approximate Bayesian Analysis: }{
+     \item{Approximate Bayesian Analysis }{ \ }
 
-       Try \code{example(linear.bayes)}, then look at the help page for it.}
+     \describe{
+       \item{\code{\link{linear.bayes}}}{
+	 For a good starting point try \code{example(linear.bayes)}}}
+   }
+   }
 
- }
- }
 \author{Charles C. Berry \email{cberry@ucsd.edu}}
 
-
-\keyword{Introduction }
+\keyword{regression,models}

man/adjust.linear.bayes.Rd

@@ -36,4 +36,4 @@ adjust.linear.bayes(lbo, ana.obj=lbo$call$ana.obj, ...)
   this can require a very long time to run.}
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
 \seealso{\code{\link{linear.bayes}}}
-\keyword{ bqtl }
+\keyword{ regression }

man/bqtl-internal.Rd

@@ -20,4 +20,4 @@ unique.config(swap.obj)
 \details{
   These are not to be called by the user.
 }
-\keyword{bqtl}
+\keyword{utilities}

man/bqtl.Rd

@@ -85,4 +85,6 @@ round( regr.coef.table[,"Value"] +  # coefs inside 95\% CI
 
 \testonly{ rm(five.gene,little.ana.bc,little.bqtl,max.loglik,
               regr.coef.table,several.epi,several.main) }
-}
+}
+\keyword{regression}
+

man/coef.bqtl.Rd

@@ -21,6 +21,4 @@ coef(bqtl.obj)
 
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
 \seealso{\code{\link{bqtl}}}
-\keyword{bqtl}
-
-
+\keyword{methods}

man/configs.Rd

@@ -92,3 +92,4 @@ map and the marker information,
 
  }
 
+\keyword{utilities, models}

man/covar.Rd

@@ -55,3 +55,4 @@ covar(x,...,scope=<see below>, method=<see below>)
    }
 
 
+\keyword{models,regression}

man/formula.bqtl.Rd

@@ -18,4 +18,4 @@ formula.bqtl(object)
 
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
 \seealso{\code{\link{bqtl}}}
-\keyword{ bqtl }
+\keyword{ methods }

man/lapadj.Rd

@@ -103,4 +103,4 @@ models.  Thesis (Ph. D.)--University of California, San Diego,
 Department of Mathematics.
   }
   \author{Charles C. Berry \email{cberry@ucsd.edu} }
-
+ \keyword{models,regression}

man/linear.bayes.Rd

@@ -85,3 +85,4 @@ plot(fitted(little.lin), residuals(little.lin))
 \testonly{rm(little.lin,little.ana.bc)}
 }
 
+\keyword{regression,models}

man/locus.Rd

@@ -100,3 +100,4 @@ of a model formula(s).
   map and the marker information.
 
 }
+\keyword{models,regression}

man/loglik.Rd

@@ -33,4 +33,4 @@ posterior(x)
 }
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
 \seealso{ \code{\link{bqtl}} }
-\keyword{bqtl}
+\keyword{models}

man/make.analysis.obj.Rd

@@ -127,4 +127,5 @@ little.ana.bc <- make.analysis.obj(little.bc.pheno$bc.phenotype,
 summary( little.ana.bc )
 
 \testonly{rm( little.ana.bc, little.bc.pheno, little.mf.5, little.bc.markers )}
-}
+}
+\keyword{manip}

man/make.loc.right.Rd

@@ -29,3 +29,4 @@ make.loc.right(marker.frame, marker.distances)
 
 }
 
+\keyword{manip}

man/make.location.prior.Rd

@@ -26,3 +26,4 @@ make.location.prior( x, add.2.end=0, normalize=TRUE )
 
 
 
+\keyword{utilities}

man/make.map.frame.Rd

@@ -25,7 +25,7 @@ morgan=100, nint=NULL, reso=NULL)
 \code{"data.frame"} or a vector or a
     data.frame with a column named \code{cM}, \code{M}, or \code{dx} or
     whose first column gives location  
-    on each chromosome in \code{100/morgan} centiMorgans (from start of
+    on each chromosome in  centiMorgans (from start of
     chromosome or Morgans if \code{M} was the column name).  It is best
     if \code{names(dx)} (for vector arguments) 
     or \code{row.names(dx)} (for data.frame arguments) give names of
@@ -87,3 +87,4 @@ plot( little.mf.5 ) # notice the 'virtual' markers added
 \testonly{ rm( little.map.dx,little.map.frame ,little.mf.5) }
 }
 
+\keyword{manip}

man/make.marker.numeric.Rd

@@ -25,3 +25,4 @@ make.marker.numeric(marker.frame, level.names=NULL)
 }
 
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
+\keyword{utilities}

man/make.regressor.matrix.Rd

@@ -33,3 +33,4 @@ A state.matrix.object - see \code{\link{make.state.matrix}} for more details
 \seealso{
   \code{\link{make.state.matrix}}
 }
+\keyword{utilities}

man/make.state.matrix.Rd

@@ -60,3 +60,4 @@ make.state.matrix(marker.frame, marker.distances, method="F2")
   It might have been better to design this array so that the third
   subscript moves fastest.  In large problems, the current structure may
   involve excessive memory access.}
+\keyword{utilities}

man/make.varcov.Rd

@@ -40,3 +40,4 @@ make.varcov(regressor.matrix, y, subset=is.finite(y), casewt=NULL)
   ill-conditioning.  Of course the rational for using the method is to
   speed the sampling, and it is very effective at doing so.} 
 
+\keyword{utilities}

man/map.index.Rd

@@ -47,5 +47,5 @@ fit.on.1 <- bqtl(bc.phenotype~locus(index.chr.1),little.ana.bc)
 summary( loglik( fit.on.1 ) )
 
 }
-\keyword{bqtl}
 
+\keyword{methods}

man/map.location.Rd

@@ -20,7 +20,7 @@ map.loc(x)
 
 \arguments{
   \item{x}{A object of class \code{map.frame},\code{analysis.object},
-\code{bqtl}, or \code{bqtl.list}
+\code{bqtl}, or \code{bqtl.list}}
   \item{\dots}{Other arguments usage depend on the class of \code{x} }
   \item{y}{A vector of row numbers or \code{map.names} specifying which
     subset of the \code{map.frame} of \code{x} is to be returned}
@@ -31,8 +31,8 @@ map.loc(x)
     in \code{chromo} will be included.)
 
   \item{map.names}{A vector of \code{map.names}}
-
-} \details{ It is often helpful to refer to genentic loci by their
+}
+\details{ It is often helpful to refer to genentic loci by their
 locations. The methods of \code{map.location} (alias \code{map.loc})
 will extract the row index, chromosome number and location, and the name
 for specified loci. For direct lookups of the loci in a \code{map.frame}
@@ -69,4 +69,4 @@ map.loc(little.ana.bc,chromo=3,cM=22)
 map.loc(little.ana.bc,"m.12")
 rm(little.ana.bc)
 }
-\keyword{bqtl}
+\keyword{\keyword{bqtl}

man/marker.fill.Rd

@@ -60,3 +60,4 @@ cbind(nint=little.nint,cM=little.map.frame$cM)[1:10,]
 rm( little.map.frame, little.nint )
 }
 % Converted by Sd2Rd version 1.10.
+\keyword{utilties}

man/marker.levels.Rd

@@ -59,3 +59,4 @@ f2.levels(Aa="H")
 bc1.levels(Aa="H")
 
 }
+\keyword{manip}

man/plot.map.frame.Rd

@@ -66,4 +66,4 @@ par(.old.par)
 \testonly{ rm(null.llk, llk, little.ana.bc, .old.par ) }
 
 }
-\keyword{bqtl}
+\keyword{hplot,methods	}

man/predict.bqtl.Rd

@@ -52,3 +52,4 @@ cbind( genotype.grid, fit.vals )                     # print them!
 
 }
 
+\keyword{methods}

man/predict.linear.bayes.Rd

@@ -40,3 +40,4 @@ hence which variable to use in ofrming residuals. So, in that case,
 
 \seealso{ \code{\link{linear.bayes}}}
 
+\keyword{methods}

man/residuals.bqtl.Rd

@@ -45,4 +45,5 @@ plot( fitted( fit.pheno ), residuals( fit.pheno) )
 
 \testonly{rm(little.ana.bc,fit.pheno)}
 
-} 
+}
+\keyword{methods}

man/summary.adj.Rd

@@ -40,3 +40,4 @@ A list with components
     Section,} 164-169. 
 }
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
+\keyword{methods}

man/summary.bqtl.Rd

@@ -34,3 +34,4 @@ return.hess=TRUE )
 summary(fit)
 \testonly{rm(little.ana.bc,fit)}
 }
+\keyword{methods}

man/summary.map.frame.Rd

@@ -22,4 +22,4 @@ summary.analysis.object(x)
  a list
 }
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
-\keyword{bqtl}
+\keyword{methods}

man/summary.swap.Rd

@@ -29,3 +29,4 @@ summary.swap(sc.obj, method=NULL, ncoef=length(sc.obj$alt.coef), nloc=sc.obj$nlo
 }
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
 
+\keyword{methods}

man/swap.Rd

@@ -93,3 +93,4 @@ plot( little.ana.bc, little.4.smry$loc.posterior, type="h",
  ylab="E(genes)" )
 rm(little.4,little.vc,little.ana.bc)
 }
+\keyword{regression}

man/swapbc1.Rd

@@ -81,3 +81,4 @@ cycle is repeated \code{nreps] times.
     Section,} 164-169.
 }
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
+\keywords{utilities}

man/swapf2.Rd

@@ -95,3 +95,4 @@ swapf2(varcov, invars, rparm, nreps, locs = <see below>>,
 }
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
 
+\keyword{utilities}

man/twohk.Rd

@@ -78,3 +78,4 @@ little.pe <- 2 * little.2$loc.2 / sum(little.2$loc.2)   #locus-wise posterior ex
 plot(little.ana.bc,little.pe,type="h",ylab="E(genes")
 rm(little.2,little.vc,little.pe,little.ana.bc)
 }
+\keyword{models}

man/twohkbc1.Rd

@@ -70,3 +70,4 @@ combo.prior=<see below>)
   quantitative trait loci in line crosses using flanking
   markers. \emph{Heredity} \bold{69},315-324. } 
 \author{Charles C. Berry \email{cberry@ucsd.edu} }
+\keyword{utilities}

man/update.bqtl.Rd

@@ -47,3 +47,4 @@ image( 1:21, 44:64, little.res )
 rm(little.ana.bc, little.update, little.res  )
 }
 
+\keyword{models}

man/varcov.Rd

@@ -42,4 +42,5 @@ varcov(x, ana.obj, partial=NULL, scope=<see below>}
   added to diagonal of \code{varcov()$var.x} and this reduces the
   ill-conditioning.  Of course the rational for using the method is to
   speed the sampling, and it is very effective at doing so.}
-\seealso{The examples in \code{\link{swap}} and \code{\link{twohk}}.}
+\seealso{The examples in \code{\link{swap}} and \code{\link{twohk}}.}
+\keyword{utilities}