elementLengths was renamed -> elementNROWS in S4Vectors (new name ref…

…lects TRUE

semantic, old name will be deprecated soon)


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RnBeads@113044 bc3139a8-67e5-0310-9ffc-ced21a209358

DESCRIPTION

@@ -10,7 +10,7 @@ Authors@R: c(
     person("Fabian", "Mueller", email = "[email protected]",
     role = c("aut", "cre")))
 Date: 2016-01-13
-Version: 1.3.5
+Version: 1.3.6
 Suggests:
     Category,
     GEOquery,
@@ -43,6 +43,7 @@ Suggests:
 Depends:
     R (>= 3.0.0),
     BiocGenerics,
+    S4Vectors (>= 0.9.25),
     GenomicRanges,
     MASS,
     RColorBrewer,

NAMESPACE

@@ -238,6 +238,7 @@ import(GenomicRanges)
 import(IRanges)
 import(MASS)
 import(RColorBrewer)
+import(S4Vectors)
 import(cluster)
 import(ff)
 import(fields)

R/RnBeads-package.R

@@ -7,7 +7,7 @@
 #' The complete analysis can be performed by calling the function \code{\link{rnb.run.analysis}}. 
 #' 
 #' @references Yassen Assenov*, Fabian Mueller*, Pavlo Lutsik*, Joern Walter, Thomas Lengauer and Christoph Bock (2014) Compehensive Analysis of DNA Methylation Data with RnBeads, Nature Methods, 11(11):1138-1140.
-#' @import methods MASS cluster RColorBrewer fields ggplot2 IRanges GenomicRanges methylumi ff gridExtra limma
+#' @import methods MASS cluster RColorBrewer fields ggplot2 S4Vectors IRanges GenomicRanges methylumi ff gridExtra limma
 #' @importFrom BiocGenerics annotation
 #' @importFrom BiocGenerics annotation<-
 #' @importFrom illuminaio readIDAT

R/annotations.R

@@ -484,9 +484,9 @@ load.annotations <- function(assembly = NULL, sites = NULL) {
 			for (a.name in updated) {
 				.rnb.annotations[[assembly]][["lengths"]][, a.name] <- 0L
 				if (a.name %in% names(genome.info$regions)) {
-					a.lengths <- elementLengths(genome.info$regions[[a.name]])
+					a.lengths <- elementNROWS(genome.info$regions[[a.name]])
 				} else { # a.name %in% names(genome.info$sites)
-					a.lengths <- elementLengths(genome.info$sites[[a.name]])
+					a.lengths <- elementNROWS(genome.info$sites[[a.name]])
 				}
 				.rnb.annotations[[assembly]][["lengths"]][names(a.lengths), a.name] <- a.lengths
 			}
@@ -535,7 +535,7 @@ rnb.update.annotation.infos <- function(type, assembly) {
 	CHROMOSOMES <- names(.rnb.annotations[[assembly]][['CHROMOSOMES']])
 	a.lengths.full <- rep.int(0L, length(CHROMOSOMES))
 	names(a.lengths.full) <- CHROMOSOMES
-	a.lengths <- elementLengths(.rnb.annotations[[assembly]][["regions"]][[type]])
+	a.lengths <- elementNROWS(.rnb.annotations[[assembly]][["regions"]][[type]])
 	a.lengths.full[names(a.lengths)] <- a.lengths
 	i.type <- which(colnames(.rnb.annotations[[assembly]][["lengths"]]) == type)
 	if (length(i.type) == 0) {

R/normalization.R

@@ -495,7 +495,7 @@ rnb.execute.normalization<-function(
 
 		if(inherits(object,"MethyLumiSet")){
 
-			if(nrow(methylated(object))<sum(elementLengths(rnb.get.annotation("probes450"))) ||
+			if(nrow(methylated(object))<sum(elementNROWS(rnb.get.annotation("probes450"))) ||
 					sum(is.na(methylated(object)))>0 || sum(is.na(unmethylated(object)))>0){
 				rnb.warning("Funtional normalization is only supported for unfiltered data sets where intensity values are present for all probes. Skipping normalization")
 				object<-as(object, "RnBeadRawSet")
@@ -508,7 +508,7 @@ rnb.execute.normalization<-function(
 
 		}else if(inherits(object,"RnBeadRawSet")){
 
-			if(nrow(sites(object))<sum(elementLengths(rnb.get.annotation("probes450"))) ||
+			if(nrow(sites(object))<sum(elementNROWS(rnb.get.annotation("probes450"))) ||
 					sum(is.na(M(object)))>0 || sum(is.na(U(object)))>0){
 				rnb.warning("Funtional normalization is only supported for unfiltered data sets where intensity values are present for all probes. Skipping normalization")
 				object@status$normalized<-"none"
@@ -823,7 +823,7 @@ rnb.section.normalization <- function(report, rnb.set, betas.raw = NULL) {
 		txt <- c(txt, "The measurements in this dataset were not normalized after ",
 			ifelse(txt == "", "loading", "background subtraction"), ".")
 		if(rnb.getOption("normalization.method")=="minfi.funnorm"){
-			if(nrow(sites(rnb.set))<sum(elementLengths(rnb.get.annotation("probes450")))){
+			if(nrow(sites(rnb.set))<sum(elementNROWS(rnb.get.annotation("probes450")))){
 				txt<-c(txt, "The desired normalization method \"minfi.funnorm\" was not applied since the data set did not
 					contain information for all probes. This is most likely because of the preceding quality filtering steps.",
 					"In order to apply minfi.funnorm in the full RnBeads analysis you should disable SNP filtering and Greedycut.",