feat: new methy conver function

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dsOmics
 Type: Package
 Title: DataSHIELD server site Omic functions
-Version: 1.0.18
+Version: 1.0.18-2
 Date: 2021-07-08
 Authors@R: c(person("Yannick", "Marcon", , "yannick.marcon@obiba.org", role = "aut"),
   person("Xavier", "Esriba-Montagut", , "xavier.escriba@isglobal.org", role = "aut"),
@@ -78,7 +78,8 @@ AssignMethods:
    subsetGenoDS,
    geno_pca_pooled_addPCDS,
    geno_pca_pooled_addPC2GenoDS,
-   pDataDS
+   pDataDS,
+   methylation_array_convertDS
 Options:
     default.nfilter.diffP.epsilon=3,
     default.nfilter.diffP.resampleN=3,
@@ -88,5 +89,5 @@ License: MIT + file LICENSE
 biocViews: DNAMethylation, Microarray, Software, WholeGenome, GWAS, Non-disclosive
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 7.2.2.9000
+RoxygenNote: 7.2.3
 Encoding: UTF-8

NAMESPACE

@@ -44,6 +44,7 @@ export(getVariable)
 export(limmaDS)
 export(limmaDS2)
 export(make_valid_namesDS)
+export(methylation_array_convertDS)
 export(nFeaturesDS)
 export(nSamplesDS)
 export(pDataDS)

R/methylation_array_convertDS.R

@@ -0,0 +1,21 @@
+#' @title Convert methylation arrays
+#'
+#' @param eSet `ExpressionSet` to convert
+#' @param objective_array `character` Array to which conver (`"450k"` or `"epic"`)
+#'
+#' @return `ExpressionSet` converted
+#' @export
+#'
+methylation_array_convertDS <- function(eSet, objective_array){
+
+  if(objective_array == "450k"){
+    cpgs <- rownames(IlluminaHumanMethylation450kanno.ilmn12.hg19::SNPs.Illumina)
+  } else if (objective_array == "epic"){
+    cpgs <- rownames(IlluminaHumanMethylationEPICanno.ilm10b2.hg19::SNPs.Illumina)
+  } else {
+    stop()
+  }
+
+  eSet_converted <- eSet[rownames(eSet) %in% cpgs, ]
+  return(eSet_converted)
+}