Update data_processing.R

data_processing.R

@@ -127,29 +127,6 @@ collections_ma <- rbind(numof_control_ma, numof_treatment_ma, numof_series_ma)
 collections_ma <- as.data.frame(collections_ma)
 colnames(collections_ma) <- colnames_microarray
 
-# GSEアクセッションIDにハイパーリンクをつける
-list_microarray2 <- list_microarray
-list_seriesm <- sapply(list_microarray, "[[", "Series")
-names(list_seriesm) <- names(list_microarray)
-
-obj <- names(list_microarray)
-for (i in obj) {
-  targets_series <- which(!duplicated(list_seriesm[[i]]))
-  comma_splited <- targets_series[grepl(",", list_microarray[[i]]$Series[targets_series])]
-  list_microarray2[[i]]$Series[targets_series] <- paste0("<a href = https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=", 
-                                                        list_microarray[[i]]$Series[targets_series], " ", blank, ">",
-                                                        list_microarray[[i]]$Series[targets_series], "</a>")
-  if (length(comma_splited) > 0) { # (GSEXXXX, GSEXXXX)の場合はそれぞれにつける
-    list_microarray2[[i]]$Series[comma_splited] <- paste0("<a href = https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=", 
-                                                         strsplit(list_microarray[[i]]$Series[comma_splited], ", ")[[1]][1], " ", blank, ">",
-                                                         strsplit(list_microarray[[i]]$Series[comma_splited], ", ")[[1]][1], "</a>, ",
-                                                         "<a href = https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=", 
-                                                         strsplit(list_microarray[[i]]$Series[comma_splited], ", ")[[1]][2], " ", blank, ">",
-                                                         strsplit(list_microarray[[i]]$Series[comma_splited], ", ")[[1]][2], "</a>")
-  }
-  assign(i, list_microarray2[[i]])
-}
-
 # RNA-Seq #########################################################
 
 ## Atlas ####
@@ -287,29 +264,6 @@ CollectionsInfo <- function(stress) {
   ))
 }
 
-# GSEアクセッションIDにハイパーリンクをつける
-list_rnaseq2 <- list_rnaseq
-list_seriesm <- sapply(list_rnaseq, "[[", "Series")
-names(list_seriesm) <- names(list_rnaseq)
-
-obj <- names(list_rnaseq)
-for (i in obj) {
-  targets_series <- which(!duplicated(list_seriesm[[i]]))
-  comma_splited <- targets_series[grepl(",", list_rnaseq[[i]]$Series[targets_series])]
-  list_rnaseq2[[i]]$Series[targets_series] <- paste0("<a href = https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=", 
-                                                         list_rnaseq[[i]]$Series[targets_series], " ", blank, ">",
-                                                         list_rnaseq[[i]]$Series[targets_series], "</a>")
-  if (length(comma_splited) > 0) { # (GSEXXXX, GSEXXXX)の場合はそれぞれにつける
-    list_rnaseq2[[i]]$Series[comma_splited] <- paste0("<a href = https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=", 
-                                                          strsplit(list_rnaseq[[i]]$Series[comma_splited], ", ")[[1]][1], " ", blank, ">",
-                                                          strsplit(list_rnaseq[[i]]$Series[comma_splited], ", ")[[1]][1], "</a>, ",
-                                                          "<a href = https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=", 
-                                                          strsplit(list_rnaseq[[i]]$Series[comma_splited], ", ")[[1]][2], " ", blank, ">",
-                                                          strsplit(list_rnaseq[[i]]$Series[comma_splited], ", ")[[1]][2], "</a>")
-  }
-  assign(i, list_rnaseq2[[i]])
-}
-
 # GMTファイルを読み込む
 positiveSRscore_ma <- read.gmt("gmt/microarray/positiveSRscore_ma.gmt")
 negativeSRscore_ma <- read.gmt("gmt/microarray/negativeSRscore_ma.gmt")