first commit

README

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+BrainStars API client for R
+
+Itoshi NIKAIDO <dritoshi@gmail.com>
+Copyright (C) 2009. Itoshi NIKAIDO. GPL 2
+
+This R library can search and get gene expression data and plots
+from BrainStars (or B*, http://brainstars.org/).
+
+BrainStars is a quantitative expression database of the adult
+mouse brain. The database has genome-wide expression profile at 51
+adult mouse CNS regions.
+
+For 51 CNS regions, slices (0.5-mm thick) of mouse brain were cut on a
+Mouse Brain Matrix, frozen, and the specific regions were punched out
+bilaterally with a microdissecting needle (gauge 0.5 mm) under a
+stereomicroscope. For each region, we took samples every 4 hours,
+starting at ZT0 (Zeitgaber time 0; the time of lights on), for 24
+hours (6 time-point samples for each region), and we pooled the
+samples from the different time points. We independently sampled each
+region twice (n=2).
+
+These samples were purified their RNA, and measured with Affymetrix
+GeneChip Mouse Genome 430 2.0 arrays. Expression values were then
+summarized with the RMA method. After several analysis with the
+expression data, the data and analysis results were stored in the
+BrainStars database.

Rakefile

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+task :default => [:demo]
+
+desc "Run demo"
+task :demo do
+  sh "R -q -f run_brainstars.r"
+end

brainstars.r

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+#
+# R Library for BrainStars http://brainstars.org/
+#
+# Itoshi NIKAIDO <dritoshi@gmail.com>
+# Copyright (C) 2009. Itoshi NIKAIDO. GPL 2
+#
+
+getBrainStarsExpression <- function(gene) {
+  base.url    <- "http://brainstars.org/probeset/"
+  url.options <- "/exprvalues.csv"
+  url         <- paste(base.url, gene, url.options, sep="")
+
+  expr <- read.csv(url, row.names=1)
+  return(expr)
+}
+
+getBrainStarsFigure <- function(gene, url.option) {
+  require("RCurl")
+
+  base.url    <- "http://brainstars.org/probeset/"
+  url.option.list <- c("exprgraph", "exprmap", "switchgraph", "switchhist", "switchmap")
+
+  if (sum(url.option.list == url.option) != 1) {
+    error.meg <- "Specify figure type."
+    error.meg <- paste(error.meg, paste(url.option.list, collapse=", "))
+    stop(warn=error.meg)
+  }
+
+  cat("Downloading...\n")
+  url         <- paste(base.url, gene, "/", url.option, ".png", sep="")
+  file.name   <- paste(gene, ".", url.option, ".png", sep="")
+  plot <- getBinaryURL(url)
+  cat("Done.\n")
+
+  writeBin(plot, file.name)
+  invisible(plot)
+}
+
+getBrainStarsSearch <- function(keyword) {
+  require("RCurl")
+
+  base.url    <- "http://brainstars.org/search/"
+
+#  if (sum(keyword) != 1) {
+#    error.meg <- "Input keyword type."
+#    error.meg <- paste(error.meg, paste(keyword, collapse=", "))
+#    stop(warn=error.meg)
+#  }
+
+  cat("Downloading...\n")
+  url         <- paste(base.url, keyword, sep="")
+  cat("Done.\n")
+  results <- getURL(url)
+  results <- unlist(strsplit(results, "\n"))
+  return(results)
+
+#  writeBin(plot, file.name)
+#  invisible(plot)
+}
+
+getBrainStarsMarker <- function(keyword) {
+  require("RCurl")
+
+  base.url    <- "http://brainstars.org/marker/"
+  json.option <- "?content-type=application/json"
+
+  cat("Downloading...\n")
+  url         <- paste(base.url, keyword, json.option, sep="")
+  cat(url, "\n")
+  cat("Done.\n")
+  results <- getURL(url)
+  #results <- unlist(strsplit(results, "\n"))
+  return(results)
+}

run_brainstars.r

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+source("brainstars.r")
+
+# Search API
+receptors     <- getBrainStarsSearch("receptor/10,5")
+num.receptors <- getBrainStarsSearch("receptor/count")
+cat(receptors, "\n")
+cat(num.receptors, "\n")
+
+# Marker API
+r.json <- getBrainStarsMarker("high/LS/count")
+cat(r.json, "\n")
+
+# Expression API
+expression <- getBrainStarsExpression("1439627_at") 
+print(expression)
+
+# Graph API
+getBrainStarsFigure("1439627_at", "exprgraph")
+getBrainStarsFigure("1439627_at", "exprmap")
+getBrainStarsFigure("1439627_at", "switchgraph")
+#getBrainStarsFigure("1439627_at", "switchhist")
+getBrainStarsFigure("1439627_at", "switchmap")