[Genabel-commits] r1355 - pkg/GenABEL/R

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-10-30 17:40:46 +0100 (Wed, 30 Oct 2013)
New Revision: 1355

Modified:
   pkg/GenABEL/R/grammar.R
Log:
In GenABEL's grammar.R:

- Small corrections in the code layout of the example code 
- Minor typo fixed in a comment and the intro text


Modified: pkg/GenABEL/R/grammar.R
===================================================================
--- pkg/GenABEL/R/grammar.R	2013-10-30 16:34:41 UTC (rev 1354)
+++ pkg/GenABEL/R/grammar.R	2013-10-30 16:40:46 UTC (rev 1355)
@@ -1,6 +1,6 @@
 #' GRAMMAR test for association in samples with genetic structure
 #'
-#' Fast approximate test for association between a trait and genetic polymorphism,
+#' Fast approximate test for association between a trait and genetic polymorphisms,
 #' in samples with genetic sub-structure (e.g. relatives). The function implements
 #' several varieties of GRAMMAR ('gamma','gc', and 'raw').
 #'
@@ -9,21 +9,21 @@
 #' is conservative and generates biased estimates of regression coefficients.
 #'
 #' With 'gc' argument, the GRAMMAR-GC (Amin et al., 2007) is implemented.
-#' This method solves conservativity of the test, but the Genomic Control (GC)
+#' This method solves the conservativity of the test, but the Genomic Control (GC)
 #' lambda is by definition "1" and can not serve as an indicator of goodness of
 #' the model; also, the estimates of regression coefficients are biased (the
 #' same as in 'raw' GRAMMAR).
 #'
 #' GRAMMAR-Gamma (default 'gamma' argument) solves these problems, producing
-#' correct distribution of the test statistic, interpretable value of GC Lambda,
+#' a correct distribution of the test statistic, interpretable value of GC Lambda,
 #' and unbiased estimates of the regression coefficients. All together, the
 #' default 'gamma' method is recommended for use.
 #'
 #' @param polyObject object returned by \code{\link{polygenic}} function
 #' @param data object of \code{\link{gwaa.data-class}}
 #' @param method to be used, one of 'gamma','gc', or 'raw'
-#' @param propPs proportion of non-corrected P-values used to estimate the inflation factor Lambda,
-#' passed directly to the \code{\link{estlambda}}
+#' @param propPs proportion of non-corrected P-values used to estimate
+#' the inflation factor Lambda, passed directly to the \code{\link{estlambda}}
 #' @param ... arguments passed to the function used for computations,
 #' (\code{\link{qtscore}})
 #'
@@ -52,19 +52,19 @@
 #' @examples
 #' # Using clean ge03d2 data
 #' data(ge03d2.clean)
-#' #take small piece for speed
+#' # take only a small piece for speed
 #' ge03d2.clean <- ge03d2.clean[1:200,]
 #' # estimate genomic kinship
-#' gkin <- ibs(ge03d2.clean[,sample(autosomal(ge03d2.clean),1000)],w="freq")
-#' # perform polygneic analysis
-#' h2ht <- polygenic(height ~ sex + age,kin=gkin,ge03d2.clean)
+#' gkin <- ibs(ge03d2.clean[,sample(autosomal(ge03d2.clean),1000)], w="freq")
+#' # perform polygenic analysis
+#' h2ht <- polygenic(height ~ sex + age, kin=gkin, ge03d2.clean)
 #' h2ht$est
 #' # compute mmscore stats
-#' mm <- mmscore(h2ht,data=ge03d2.clean)
+#' mm <- mmscore(h2ht, data=ge03d2.clean)
 #' # compute grammar-gc
-#' grGc <- grammar(h2ht,data=ge03d2.clean,method="gc")
-#' #compute grammar-gamma
-#' grGamma <- grammar(h2ht,data=ge03d2.clean,method="gamma")
+#' grGc <- grammar(h2ht, data=ge03d2.clean, method="gc")
+#' # compute grammar-gamma
+#' grGamma <- grammar(h2ht, data=ge03d2.clean, method="gamma")
 #' # compare lambdas
 #' lambda(mm)
 #' estlambda(mm[,"chi2.1df"])
@@ -72,7 +72,7 @@
 #' estlambda(grGamma[,"chi2.1df"])
 #' lambda(grGc)
 #' estlambda(grGc[,"chi2.1df"])
-#' #compare top results
+#' # compare top results
 #' summary(mm)
 #' summary(grGamma)
 #' summary(grGc)
@@ -119,7 +119,7 @@
         stop("method should be one of 'gamma','gc', or 'raw'")
     }
 
-    ## set uncorrectet stats to NA to avoid confusion
+    ## set uncorrected stats to NA to avoid confusion
     out at results[,"effAB"] <- out at results[,"effBB"] <- out at results[,"chi2.2df"] <-
         out at results[,"P2df"] <- NA
     out at call <- match.call()