version 0.1-6

cran · Jul 24, 2013 · ac6b48d · ac6b48d
1 parent 8c32412
commit ac6b48d
Show file tree

Hide file tree

Showing 8 changed files with 78 additions and 51 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,14 @@
 Package: HapEstXXR
-Version: 0.1-5
-Date: 2013-08-03
-Title: HapEstXXR
+Version: 0.1-6
+Date: July 24, 2013
+Title: Multi-locus stepwise regression (MSR)
 Author: Sven Knueppel and Klaus Rohde
 Maintainer: Sven Knueppel <sven.knueppel@dife.de>
 Depends: survival
 Description: Multi-locus marker analysis
 License: LGPL (>= 2.1)
 LazyLoad: TRUE
 Repository: CRAN
-Packaged: 2013-03-16 13:20:57 UTC; Sven
+Packaged: 2013-07-24 04:48:57 UTC; Sven
 NeedsCompilation: yes
-Date/Publication: 2013-03-16 14:59:11
+Date/Publication: 2013-07-24 08:53:49
diff --git a/MD5 b/MD5
@@ -1,4 +1,4 @@
-018e4711a6512ee5f39855ef3037f06d *DESCRIPTION
+ea2e9cf43e572b82741d90a8ba33b69d *DESCRIPTION
 266fac7ae5c891f4c8296537dd9ead12 *NAMESPACE
 7a27c9428493baf14ac86dfdd999f9de *R/allele1to2.R
 d915eced680d427f786cff3f8dc8cf25 *R/allele1toR.R
@@ -14,7 +14,7 @@ e36692655bc3c7133f0c8c5495ae2440 *R/itegeppXXR.R
 78d7c969d01fe9c5e8eb4b95bc27b04f *R/maf.R
 5811f03b7302c49848030dc7f5a67503 *R/makeHaploviewInputFile.R
 737dd89228644ebef77677592cdc1489 *R/makePlinkInputFile.R
-793e6e82b098a4d6bcc9b5ce864e70cc *R/msr.R
+d82684bbf9078b7600d2759e64a9e3bb *R/msr.R
 c2a0bd47bf19ed7df62f1e1d8ae9c0f4 *R/msr.binomial.forward.adjusted.R
 8f2482cca9224091a748295b05b0d171 *R/msr.binomial.forward.unadjusted.R
 42fc4974a7332f488d2fe7ec805b5688 *R/msr.binomial.haplotype.test.adjusted.R
@@ -29,7 +29,7 @@ f56ba600403b7bbc920b2478b631c56e *R/multi.snp.test.R
 9eb3a5a3555ccdcd72ee8133af01fcca *R/powerset.R
 b57895f30c1cce9ea0d020dc37ed8cf2 *R/read.data.R
 f50681b187a1cbd1e2f62b36d33472d0 *R/read.haploview.R
-cc7a0978ef64e1ca3ff07a10165b6553 *R/single.haplotype.test.R
+bd62c5a762106da8c7a4bad5ea8e08c8 *R/single.haplotype.test.R
 c0ebd3fc6042b02aae19509dc664ed35 *R/single.haplotype.test.binomial.R
 aeae94d6b6b5d1e5618c50d1c55d3bdc *R/single.haplotype.test.families.R
 d48003df62c633a3859b3ef398873e50 *R/single.haplotype.test.gaussian.R
@@ -49,14 +49,14 @@ ee72af4a6bfe051e4671639c63ba2e1a *man/catt.Rd
 84f3caced323826f902729158dc09dec *man/maf.Rd
 8481ea65ab1a75e6fe1b8e142a30ea6f *man/makeHaploviewInputFile.Rd
 17f8dddcd69bd61ef3f5308133fe943e *man/makePlinkInputFile.Rd
-9ef194e51223ed02f82c1e075ac19ccb *man/msr.Rd
-6ac3d7740823c0af8bdf6ca2a1b262db *man/multi.snp.test.Rd
+e3947aa312bc9fc7a7a1d5d3bed8b2eb *man/msr.Rd
+2654fdba8f585a845062e4943afb6f1b *man/multi.snp.test.Rd
 4e64b89846dabd747caf277e404d3418 *man/order.families.Rd
 56559a70e219118fe6443ffa5d6ec683 *man/powerset.Rd
 c9e5b3f8305ce12d9e9793a0cd8c7bbb *man/read.data.Rd
 c7054461e122093016c30189cef45c69 *man/read.haploview.Rd
-ccc6637f0eefc5b5c60204d7bc8c94fc *man/single.haplotype.test.Rd
-35230c36146a9ba8496a9751a2aa48eb *man/single.snp.test.Rd
+ae9962d7c2c68a20146c9b30af25be49 *man/single.haplotype.test.Rd
+f7d6e8297947695d19a5e71a6f11e295 *man/single.snp.test.Rd
 7742135e288e128650d56ca54c882596 *src/HapRshort.c
 de9fa714586addcc87ed9534abc1ece2 *src/bool.h
 c1b30846a6afbab9b55f300ae7ee954b *src/create_pattern_matrix.c

diff --git a/R/msr.R b/R/msr.R
@@ -1,9 +1,9 @@
 msr <-
-function (  famid , patid , fid , mid , snps, trait,
-    adj.var=NA , lim =0.05, maxSNP = 3 ,
-    nt = 10, pair.begin = FALSE, pattern.begin.mat=NA,
+function(famid, patid, fid, mid, snps, trait,
+    adj.var = NA, lim = 0.05, maxSNP = 3,
+    nt = 10, pair.begin = FALSE, pattern.begin.mat = NA,
     type = "gaussian" ,
-    baseline.hap="max" , min.count=10 , sort=F )
+    baseline.hap = "max", min.count = 10, sort = F)
 {
 
     # init input

diff --git a/R/single.haplotype.test.R b/R/single.haplotype.test.R
@@ -87,17 +87,35 @@ function ( snps, trait, famid , patid , fid , mid ,
     } else {
       cat ("Number of covariates:  ",dim(adj.var)[2],"\n\n",sep="" )
     }
-
   }
 
   ############################
   # single haplotype analysis
 
   switch ( type,
-           gaussian = res <- single.haplotype.test.gaussian ( snps, trait, adj.var=adj.var , lim=lim ) ,
-           binomial = res <- single.haplotype.test.binomial (  snps, trait, adj.var=adj.var , lim = lim ,
-               baseline.hap="max", do.hap.specific.test=T ,  min.count=min.count , alpha=alpha ) ,
-           families   = res <- single.haplotype.test.families ( snps, trait, famid , patid , fid , mid , lim=lim ) ,
+           gaussian = res <- single.haplotype.test.gaussian(snps,
+                                                            trait,
+                                                            adj.var = adj.var,
+                                                            lim = lim, 
+                                                            baseline.hap = "max",
+                                                            do.hap.specific.test = TRUE,
+                                                            min.count = min.count,
+                                                            alpha = alpha),
+           binomial = res <- single.haplotype.test.binomial(snps,
+                                                            trait,
+                                                            adj.var = adj.var,
+                                                            lim = lim, 
+                                                            baseline.hap = "max",
+                                                            do.hap.specific.test = TRUE,
+                                                            min.count = min.count,
+                                                            alpha = alpha) ,
+           families   = res <- single.haplotype.test.families(snps,
+                                                              trait,
+                                                              famid,
+                                                              patid,
+                                                              fid,
+                                                              mid,
+                                                              lim = lim ) ,
            survival = { print("not ready!") ; stop("end") }  )
 
  return ( res )

diff --git a/man/msr.Rd b/man/msr.Rd
@@ -1,9 +1,3 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% library(HapEstXXR)
-% Created: November 30, 2011
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
 \name{msr}
 \alias{msr}
 \alias{msr.binomial.forward.adjusted}
@@ -14,17 +8,17 @@
 \alias{msr.gaussian.haplotype.test.unadjusted}
 \alias{msr.families.unadjusted}
 \alias{msr.gaussian.forward.adjusted}
-\alias{msr.gaussian.forward.unadjusted} 
-\title{ Multi-locus stepwise regression (MSR)}
+\alias{msr.gaussian.forward.unadjusted}
+\title{Multi-locus stepwise regression}
 \description{
   Stepwise regression for snp selection and haplotype testing
 }
 \usage{
-msr ( famid, patid, fid, mid, snps, trait, adj.var = NA,
-      lim = 0.05, maxSNP = 3, nt = 10, pair.begin = FALSE,
-      pattern.begin.mat = NA, 
-      type = "gaussian", baseline.hap = "max",
-      min.count = 10, sort=F )
+msr(famid, patid, fid, mid, snps, trait,
+    adj.var = NA, lim = 0.05, maxSNP = 3,
+    nt = 10, pair.begin = FALSE, pattern.begin.mat = NA,
+    type = "gaussian" ,
+    baseline.hap = "max", min.count = 10, sort = F)
 }
 \arguments{
   \item{famid}{vector; Identifier for every family; only need in case of type=families}
@@ -40,9 +34,10 @@ msr ( famid, patid, fid, mid, snps, trait, adj.var = NA,
   \item{pair.begin}{If true then will be begin with first 2 SNP genotypes.
                                       Attention: k SNP lead to choose(k,2)=k*(k-1)/2 possible pairs }
   \item{pattern.begin.mat}{if begin.pattern.mat is not NA then is this starting point of \code{msr}
-                                 n=No. of snp pattern, m=No. of SNPs}
+                                 n=No. of snp pattern, m=No. of SNPs}                                 
   \item{type}{type of depending variable}
-  \item{baseline.hap}{Choose baseline haplotype for statistical test to avoid singularity. "max" for most frequent haplotype and "min" for less frequent haplotype }
+  \item{baseline.hap}{Choose baseline haplotype for statistical test to avoid singularity.
+                      "max" for most frequent haplotype and "min" for less frequent haplotype }
   \item{min.count}{minimal count of rare haplotypes}
   \item{sort}{A logical value (TRUE or FALSE). If TRUE, family data will be sorted.}
 }
@@ -64,18 +59,22 @@ significance we assume a genetic effect. In case of family data the weigthed TDT
   \item{list}{for every step one component:
               SNP numbers and test details like p value.}
 }
-\author{ Sven Knueppel and Klaus Rohde }
+\author{Sven Knueppel and Klaus Rohde}
 \references{
 Excoffier L, Slatkin M. Mol Biol Evol. 1995 Sep;12(5):921-7.
 
 Rohde K, Fuerst R. Hum Hered. 2003;56(1-3):41-7.
 
 Rohde K, Fuerst R. Hum Mutat. 2001 Apr;17(4):289-95.
 
-Knueppel S, Rohde K et al. Multi-locus stepwise regression: A haplotype-based
-stepwise algorithm to find haplotypes associated with genetic phenotypes.
-[in praparation]
-                                          }
-\keyword{ stepwise regression }
-\keyword{ haplotypes }
+Knueppel S, Esparza-Gordillo J, Marenholz I, Holzhuetter HG,
+
+Bauerfeind A, Ruether A, Weidinger S, Lee Y-A, Rohde K.
+
+Multi-locus stepwise regression: a haplotype-based algorithm
 
+for finding genetic associations applied to atopic dermatitis.
+
+BMC Med Genet 2012;13(1):8.
+}
+\keyword{stepwise regression}
diff --git a/man/multi.snp.test.Rd b/man/multi.snp.test.Rd
@@ -10,7 +10,7 @@
 Internal function used for multi-locus associations tests.
 }
 \description{
-This function is used for internal computations. You should not used use it, but you can.
+This function is used for internal computations. You should not use it, but you could.
 }
 \usage{
 multi.snp.test ( y , x , x.adj=NULL ,

diff --git a/man/single.haplotype.test.Rd b/man/single.haplotype.test.Rd
@@ -66,10 +66,15 @@ single haplotype test
 
    Rohde K, Fuerst R. Hum Mutat. 2001 Apr;17(4):289-95.
 
-Knueppel S, Rohde K et al. Multi-locus stepwise regression: A haplotype-based
-stepwise algorithm to find haplotypes associated with genetic phenotypes.
-[in praparation]
-
+Knueppel S, Esparza-Gordillo J, Marenholz I, Holzhuetter HG,
+
+Bauerfeind A, Ruether A, Weidinger S, Lee Y-A, Rohde K.
+
+Multi-locus stepwise regression: a haplotype-based algorithm
+
+for finding genetic associations applied to atopic dermatitis.
+
+BMC Med Genet 2012;13(1):8.
 }
 \author{
   Sven Knueppel and Klaus Rohde

diff --git a/man/single.snp.test.Rd b/man/single.snp.test.Rd
@@ -87,10 +87,15 @@ As genetic effect the allele dosis (0, 1, 2) is modelled.
  \item{aic}{Akaike's An Information Criterion (AIC) of full model}
 }
 \references{
-Knueppel S, Rohde K et al. Multi-locus stepwise regression: A haplotype-based
-stepwise algorithm to find haplotypes associated with genetic phenotypes.
-[in praparation]
+Knueppel S, Esparza-Gordillo J, Marenholz I, Holzhuetter HG,
 
+Bauerfeind A, Ruether A, Weidinger S, Lee Y-A, Rohde K.
+
+Multi-locus stepwise regression: a haplotype-based algorithm
+
+for finding genetic associations applied to atopic dermatitis.
+
+BMC Med Genet 2012;13(1):8.
 }
 \author{
 Sven Knueppel and Klaus Rohde