geo

inst/prototype/GEO.r

@@ -0,0 +1,29 @@
+
+get_gse <- function(gseID) {
+    gsecat <- sub("\\d{3}$", "nnn", gseID)
+    gsesoft <- sprintf("%s_family.soft.gz", gseID)
+    url <- sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/soft/%s", gsecat, gseID, gsesoft)
+    yulab.utils:::mydownload(url, destfile = gsesoft)
+    GEOquery::getGEO(filename = gsesoft)
+}
+
+get_gsm <- function(gse) {
+    lapply(GEOquery::GSMList(gse), function(x) x@header$supplementary_file)
+}
+
+
+
+download_gsm <- function(gsm) {
+    for (x in gsm) {
+        destfile <- sub(".*/([^/]+)$", "\\1", x)
+        yulab.utils:::mydownload(x, destfile = destfile)
+    }
+}
+
+gseID <- "GSE123904"
+
+gse <- get_gse(gseID)
+gsm <- get_gsm(gse)
+
+download_gsm(gsm)
+