Merge pull request #24 from kkleinoros/master

convert to S4
GreenwoodLab · Dec 20, 2016 · e9da732 · e9da732
2 parents 43eaf1f + 9e15e6d
commit e9da732
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diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(print,SampleSet)
 export(agreement)
 export(fromGenStudFiles)
 export(fromRGChannelSet)
@@ -12,6 +11,7 @@ export(getRawBeta)
 export(getSnpM)
 export(plotValidationGraph)
 exportClasses(SampleSet)
+exportMethods(show)
 import(IlluminaHumanMethylation450kanno.ilmn12.hg19)
 import(IlluminaHumanMethylation450kmanifest)
 import(methods)

diff --git a/R/SampleSet.R b/R/SampleSet.R
diff --git a/R/funtoonorm.R b/R/funtoonorm.R
@@ -125,7 +125,7 @@ funtooNormApply <- function(signal, quantiles, qntllist,
 }
 
 ################################################################################
-#' Function to measure intra-replicate agreement in methylation data.
+#' Function to measure intra-replicate agreement for methylation data.
 #'
 #' @param Beta : Matrix with beta-values, rows corresponding to probes, columns
 #' corresponding to samples.  

diff --git a/man/SampleSet-class.Rd b/man/SampleSet-class.Rd
diff --git a/man/agreement.Rd b/man/agreement.Rd
diff --git a/man/fromGenStudFiles.Rd b/man/fromGenStudFiles.Rd
diff --git a/man/fromRGChannelSet.Rd b/man/fromRGChannelSet.Rd
diff --git a/man/funtooNorm.Rd b/man/funtooNorm.Rd
diff --git a/man/getNormBeta.Rd b/man/getNormBeta.Rd
diff --git a/man/getNormM.Rd b/man/getNormM.Rd
diff --git a/man/getRawBeta.Rd b/man/getRawBeta.Rd
diff --git a/man/getSnpM.Rd b/man/getSnpM.Rd
diff --git a/man/plotValidationGraph.Rd b/man/plotValidationGraph.Rd
diff --git a/man/print.SampleSet.Rd → man/show-SampleSet-method.Rd b/man/print.SampleSet.Rd → man/show-SampleSet-method.Rd
diff --git a/vignettes/funtooNorm.Rmd b/vignettes/funtooNorm.Rmd
@@ -25,7 +25,7 @@ knitr::opts_chunk$set(tidy = FALSE,
 ```
 
 ```{r library, echo=FALSE, results='hide', message=FALSE}
-library(minfi)
+require(minfi)
 ```
 
 #Introduction
@@ -48,7 +48,7 @@ Note that the current version of the package does not do a good job of normalizi
   different colors provide the methylated and the unmethylated 
   measurements.  
 ```  
-Therefore, we dissociate the 6 types of signals in our method :
+Therefore, we separate the 6 types of signals in our method :
 _AIGrn_, _BIGrn_, _AIRed_, _BIRed_, _AII_  and _BII_, where the __A__ (methylated) and
 __B__ (unmethylated) are on __Green__ or __Red__ channel
 depending on the 3 types : __Type I Red__, __Type I Green__ or