rbbt-marq 1.0.0

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  1. data/LICENSE +20 -0
  2. data/R/CustomDS.R +80 -0
  3. data/R/GEO.R +249 -0
  4. data/R/MA.R +359 -0
  5. data/README.rdoc +58 -0
  6. data/bin/marq_config +209 -0
  7. data/install_scripts/CustomDS/Rakefile +223 -0
  8. data/install_scripts/GEO/Rakefile +272 -0
  9. data/install_scripts/GEO/platforms/GPL100.yaml +7 -0
  10. data/install_scripts/GEO/platforms/GPL1002.yaml +7 -0
  11. data/install_scripts/GEO/platforms/GPL1007.yaml +7 -0
  12. data/install_scripts/GEO/platforms/GPL101.yaml +7 -0
  13. data/install_scripts/GEO/platforms/GPL1010.yaml +7 -0
  14. data/install_scripts/GEO/platforms/GPL1073.yaml +7 -0
  15. data/install_scripts/GEO/platforms/GPL1074.yaml +4 -0
  16. data/install_scripts/GEO/platforms/GPL1090.yaml +7 -0
  17. data/install_scripts/GEO/platforms/GPL1104.yaml +7 -0
  18. data/install_scripts/GEO/platforms/GPL118.yaml +7 -0
  19. data/install_scripts/GEO/platforms/GPL1205.yaml +4 -0
  20. data/install_scripts/GEO/platforms/GPL1211.yaml +7 -0
  21. data/install_scripts/GEO/platforms/GPL1213.yaml +7 -0
  22. data/install_scripts/GEO/platforms/GPL1219.yaml +4 -0
  23. data/install_scripts/GEO/platforms/GPL1223.yaml +7 -0
  24. data/install_scripts/GEO/platforms/GPL1226.yaml +7 -0
  25. data/install_scripts/GEO/platforms/GPL1229.yaml +7 -0
  26. data/install_scripts/GEO/platforms/GPL1230.yaml +7 -0
  27. data/install_scripts/GEO/platforms/GPL1231.yaml +7 -0
  28. data/install_scripts/GEO/platforms/GPL1232.yaml +7 -0
  29. data/install_scripts/GEO/platforms/GPL1260.yaml +4 -0
  30. data/install_scripts/GEO/platforms/GPL1261.yaml +4 -0
  31. data/install_scripts/GEO/platforms/GPL127.yaml +4 -0
  32. data/install_scripts/GEO/platforms/GPL128.yaml +7 -0
  33. data/install_scripts/GEO/platforms/GPL1290.yaml +7 -0
  34. data/install_scripts/GEO/platforms/GPL1292.yaml +7 -0
  35. data/install_scripts/GEO/platforms/GPL1293.yaml +7 -0
  36. data/install_scripts/GEO/platforms/GPL1294.yaml +7 -0
  37. data/install_scripts/GEO/platforms/GPL1295.yaml +7 -0
  38. data/install_scripts/GEO/platforms/GPL13.yaml +4 -0
  39. data/install_scripts/GEO/platforms/GPL1310.yaml +7 -0
  40. data/install_scripts/GEO/platforms/GPL1313.yaml +7 -0
  41. data/install_scripts/GEO/platforms/GPL1323.yaml +7 -0
  42. data/install_scripts/GEO/platforms/GPL1331.yaml +7 -0
  43. data/install_scripts/GEO/platforms/GPL1352.yaml +4 -0
  44. data/install_scripts/GEO/platforms/GPL1355.yaml +4 -0
  45. data/install_scripts/GEO/platforms/GPL1382.yaml +7 -0
  46. data/install_scripts/GEO/platforms/GPL1387.yaml +7 -0
  47. data/install_scripts/GEO/platforms/GPL1397.yaml +4 -0
  48. data/install_scripts/GEO/platforms/GPL14.yaml +7 -0
  49. data/install_scripts/GEO/platforms/GPL1412.yaml +7 -0
  50. data/install_scripts/GEO/platforms/GPL1415.yaml +7 -0
  51. data/install_scripts/GEO/platforms/GPL1420.yaml +7 -0
  52. data/install_scripts/GEO/platforms/GPL144.yaml +7 -0
  53. data/install_scripts/GEO/platforms/GPL1449.yaml +7 -0
  54. data/install_scripts/GEO/platforms/GPL1458.yaml +7 -0
  55. data/install_scripts/GEO/platforms/GPL1523.yaml +7 -0
  56. data/install_scripts/GEO/platforms/GPL1524.yaml +7 -0
  57. data/install_scripts/GEO/platforms/GPL1528.yaml +7 -0
  58. data/install_scripts/GEO/platforms/GPL153.yaml +7 -0
  59. data/install_scripts/GEO/platforms/GPL1530.yaml +7 -0
  60. data/install_scripts/GEO/platforms/GPL1535.yaml +4 -0
  61. data/install_scripts/GEO/platforms/GPL155.yaml +7 -0
  62. data/install_scripts/GEO/platforms/GPL163.yaml +7 -0
  63. data/install_scripts/GEO/platforms/GPL168.yaml +7 -0
  64. data/install_scripts/GEO/platforms/GPL169.yaml +7 -0
  65. data/install_scripts/GEO/platforms/GPL1704.yaml +4 -0
  66. data/install_scripts/GEO/platforms/GPL1708.yaml +7 -0
  67. data/install_scripts/GEO/platforms/GPL1739.yaml +7 -0
  68. data/install_scripts/GEO/platforms/GPL1740.yaml +4 -0
  69. data/install_scripts/GEO/platforms/GPL1749.yaml +7 -0
  70. data/install_scripts/GEO/platforms/GPL177.yaml +7 -0
  71. data/install_scripts/GEO/platforms/GPL1790.yaml +7 -0
  72. data/install_scripts/GEO/platforms/GPL1792.yaml +7 -0
  73. data/install_scripts/GEO/platforms/GPL181.yaml +7 -0
  74. data/install_scripts/GEO/platforms/GPL1818.yaml +7 -0
  75. data/install_scripts/GEO/platforms/GPL1820.yaml +4 -0
  76. data/install_scripts/GEO/platforms/GPL1823.yaml +7 -0
  77. data/install_scripts/GEO/platforms/GPL1826.yaml +7 -0
  78. data/install_scripts/GEO/platforms/GPL183.yaml +7 -0
  79. data/install_scripts/GEO/platforms/GPL1831.yaml +7 -0
  80. data/install_scripts/GEO/platforms/GPL1833.yaml +7 -0
  81. data/install_scripts/GEO/platforms/GPL1872.yaml +4 -0
  82. data/install_scripts/GEO/platforms/GPL1911.yaml +7 -0
  83. data/install_scripts/GEO/platforms/GPL1914.yaml +4 -0
  84. data/install_scripts/GEO/platforms/GPL1928.yaml +7 -0
  85. data/install_scripts/GEO/platforms/GPL1942.yaml +7 -0
  86. data/install_scripts/GEO/platforms/GPL1945.yaml +7 -0
  87. data/install_scripts/GEO/platforms/GPL1964.yaml +7 -0
  88. data/install_scripts/GEO/platforms/GPL198.yaml +4 -0
  89. data/install_scripts/GEO/platforms/GPL1981.yaml +4 -0
  90. data/install_scripts/GEO/platforms/GPL200.yaml +7 -0
  91. data/install_scripts/GEO/platforms/GPL2006.yaml +7 -0
  92. data/install_scripts/GEO/platforms/GPL201.yaml +4 -0
  93. data/install_scripts/GEO/platforms/GPL2011.yaml +7 -0
  94. data/install_scripts/GEO/platforms/GPL2026.yaml +7 -0
  95. data/install_scripts/GEO/platforms/GPL205.yaml +7 -0
  96. data/install_scripts/GEO/platforms/GPL207.yaml +7 -0
  97. data/install_scripts/GEO/platforms/GPL2136.yaml +7 -0
  98. data/install_scripts/GEO/platforms/GPL220.yaml +7 -0
  99. data/install_scripts/GEO/platforms/GPL226.yaml +7 -0
  100. data/install_scripts/GEO/platforms/GPL24.yaml +4 -0
  101. data/install_scripts/GEO/platforms/GPL246.yaml +4 -0
  102. data/install_scripts/GEO/platforms/GPL247.yaml +7 -0
  103. data/install_scripts/GEO/platforms/GPL2507.yaml +4 -0
  104. data/install_scripts/GEO/platforms/GPL2529.yaml +4 -0
  105. data/install_scripts/GEO/platforms/GPL2531.yaml +7 -0
  106. data/install_scripts/GEO/platforms/GPL254.yaml +7 -0
  107. data/install_scripts/GEO/platforms/GPL2569.yaml +7 -0
  108. data/install_scripts/GEO/platforms/GPL257.yaml +7 -0
  109. data/install_scripts/GEO/platforms/GPL2598.yaml +7 -0
  110. data/install_scripts/GEO/platforms/GPL260.yaml +7 -0
  111. data/install_scripts/GEO/platforms/GPL2614.yaml +4 -0
  112. data/install_scripts/GEO/platforms/GPL2622.yaml +7 -0
  113. data/install_scripts/GEO/platforms/GPL2623.yaml +7 -0
  114. data/install_scripts/GEO/platforms/GPL2660.yaml +7 -0
  115. data/install_scripts/GEO/platforms/GPL2670.yaml +7 -0
  116. data/install_scripts/GEO/platforms/GPL2677.yaml +7 -0
  117. data/install_scripts/GEO/platforms/GPL2700.yaml +4 -0
  118. data/install_scripts/GEO/platforms/GPL2721.yaml +7 -0
  119. data/install_scripts/GEO/platforms/GPL2727.yaml +7 -0
  120. data/install_scripts/GEO/platforms/GPL273.yaml +7 -0
  121. data/install_scripts/GEO/platforms/GPL2763.yaml +7 -0
  122. data/install_scripts/GEO/platforms/GPL2824.yaml +7 -0
  123. data/install_scripts/GEO/platforms/GPL284.yaml +7 -0
  124. data/install_scripts/GEO/platforms/GPL287.yaml +4 -0
  125. data/install_scripts/GEO/platforms/GPL2872.yaml +7 -0
  126. data/install_scripts/GEO/platforms/GPL288.yaml +4 -0
  127. data/install_scripts/GEO/platforms/GPL2883.yaml +7 -0
  128. data/install_scripts/GEO/platforms/GPL289.yaml +4 -0
  129. data/install_scripts/GEO/platforms/GPL2895.yaml +4 -0
  130. data/install_scripts/GEO/platforms/GPL2897.yaml +7 -0
  131. data/install_scripts/GEO/platforms/GPL2902.yaml +7 -0
  132. data/install_scripts/GEO/platforms/GPL2987.yaml +4 -0
  133. data/install_scripts/GEO/platforms/GPL2995.yaml +7 -0
  134. data/install_scripts/GEO/platforms/GPL3039.yaml +4 -0
  135. data/install_scripts/GEO/platforms/GPL3050.yaml +7 -0
  136. data/install_scripts/GEO/platforms/GPL3084.yaml +7 -0
  137. data/install_scripts/GEO/platforms/GPL3113.yaml +7 -0
  138. data/install_scripts/GEO/platforms/GPL317.yaml +7 -0
  139. data/install_scripts/GEO/platforms/GPL319.yaml +7 -0
  140. data/install_scripts/GEO/platforms/GPL32.yaml +4 -0
  141. data/install_scripts/GEO/platforms/GPL3222.yaml +7 -0
  142. data/install_scripts/GEO/platforms/GPL3295.yaml +7 -0
  143. data/install_scripts/GEO/platforms/GPL3305.yaml +4 -0
  144. data/install_scripts/GEO/platforms/GPL3306.yaml +7 -0
  145. data/install_scripts/GEO/platforms/GPL3307.yaml +7 -0
  146. data/install_scripts/GEO/platforms/GPL333.yaml +4 -0
  147. data/install_scripts/GEO/platforms/GPL3341.yaml +7 -0
  148. data/install_scripts/GEO/platforms/GPL3349.yaml +7 -0
  149. data/install_scripts/GEO/platforms/GPL339.yaml +4 -0
  150. data/install_scripts/GEO/platforms/GPL340.yaml +4 -0
  151. data/install_scripts/GEO/platforms/GPL3408.yaml +7 -0
  152. data/install_scripts/GEO/platforms/GPL341.yaml +4 -0
  153. data/install_scripts/GEO/platforms/GPL3415.yaml +4 -0
  154. data/install_scripts/GEO/platforms/GPL3423.yaml +7 -0
  155. data/install_scripts/GEO/platforms/GPL3440.yaml +7 -0
  156. data/install_scripts/GEO/platforms/GPL3457.yaml +4 -0
  157. data/install_scripts/GEO/platforms/GPL3504.yaml +4 -0
  158. data/install_scripts/GEO/platforms/GPL3506.yaml +4 -0
  159. data/install_scripts/GEO/platforms/GPL355.yaml +7 -0
  160. data/install_scripts/GEO/platforms/GPL3558.yaml +7 -0
  161. data/install_scripts/GEO/platforms/GPL3607.yaml +7 -0
  162. data/install_scripts/GEO/platforms/GPL368.yaml +4 -0
  163. data/install_scripts/GEO/platforms/GPL3695.yaml +7 -0
  164. data/install_scripts/GEO/platforms/GPL371.yaml +7 -0
  165. data/install_scripts/GEO/platforms/GPL3834.yaml +4 -0
  166. data/install_scripts/GEO/platforms/GPL4006.yaml +7 -0
  167. data/install_scripts/GEO/platforms/GPL4055.yaml +7 -0
  168. data/install_scripts/GEO/platforms/GPL409.yaml +7 -0
  169. data/install_scripts/GEO/platforms/GPL4191.yaml +7 -0
  170. data/install_scripts/GEO/platforms/GPL4226.yaml +7 -0
  171. data/install_scripts/GEO/platforms/GPL4371.yaml +7 -0
  172. data/install_scripts/GEO/platforms/GPL4567.yaml +4 -0
  173. data/install_scripts/GEO/platforms/GPL4685.yaml +4 -0
  174. data/install_scripts/GEO/platforms/GPL483.yaml +7 -0
  175. data/install_scripts/GEO/platforms/GPL49.yaml +7 -0
  176. data/install_scripts/GEO/platforms/GPL50.yaml +7 -0
  177. data/install_scripts/GEO/platforms/GPL500.yaml +7 -0
  178. data/install_scripts/GEO/platforms/GPL507.yaml +4 -0
  179. data/install_scripts/GEO/platforms/GPL51.yaml +7 -0
  180. data/install_scripts/GEO/platforms/GPL513.yaml +7 -0
  181. data/install_scripts/GEO/platforms/GPL519.yaml +7 -0
  182. data/install_scripts/GEO/platforms/GPL52.yaml +7 -0
  183. data/install_scripts/GEO/platforms/GPL529.yaml +7 -0
  184. data/install_scripts/GEO/platforms/GPL53.yaml +7 -0
  185. data/install_scripts/GEO/platforms/GPL5356.yaml +7 -0
  186. data/install_scripts/GEO/platforms/GPL538.yaml +7 -0
  187. data/install_scripts/GEO/platforms/GPL54.yaml +7 -0
  188. data/install_scripts/GEO/platforms/GPL543.yaml +7 -0
  189. data/install_scripts/GEO/platforms/GPL544.yaml +7 -0
  190. data/install_scripts/GEO/platforms/GPL545.yaml +7 -0
  191. data/install_scripts/GEO/platforms/GPL546.yaml +7 -0
  192. data/install_scripts/GEO/platforms/GPL547.yaml +7 -0
  193. data/install_scripts/GEO/platforms/GPL549.yaml +7 -0
  194. data/install_scripts/GEO/platforms/GPL550.yaml +4 -0
  195. data/install_scripts/GEO/platforms/GPL56.yaml +7 -0
  196. data/install_scripts/GEO/platforms/GPL560.yaml +4 -0
  197. data/install_scripts/GEO/platforms/GPL564.yaml +7 -0
  198. data/install_scripts/GEO/platforms/GPL57.yaml +7 -0
  199. data/install_scripts/GEO/platforms/GPL570.yaml +4 -0
  200. data/install_scripts/GEO/platforms/GPL571.yaml +4 -0
  201. data/install_scripts/GEO/platforms/GPL576.yaml +7 -0
  202. data/install_scripts/GEO/platforms/GPL58.yaml +7 -0
  203. data/install_scripts/GEO/platforms/GPL5823.yaml +4 -0
  204. data/install_scripts/GEO/platforms/GPL59.yaml +7 -0
  205. data/install_scripts/GEO/platforms/GPL5915.yaml +4 -0
  206. data/install_scripts/GEO/platforms/GPL5947.yaml +7 -0
  207. data/install_scripts/GEO/platforms/GPL61.yaml +7 -0
  208. data/install_scripts/GEO/platforms/GPL64.yaml +7 -0
  209. data/install_scripts/GEO/platforms/GPL6419.yaml +7 -0
  210. data/install_scripts/GEO/platforms/GPL6424.yaml +7 -0
  211. data/install_scripts/GEO/platforms/GPL65.yaml +7 -0
  212. data/install_scripts/GEO/platforms/GPL6574.yaml +4 -0
  213. data/install_scripts/GEO/platforms/GPL6649.yaml +4 -0
  214. data/install_scripts/GEO/platforms/GPL67.yaml +7 -0
  215. data/install_scripts/GEO/platforms/GPL6720.yaml +7 -0
  216. data/install_scripts/GEO/platforms/GPL7054.yaml +4 -0
  217. data/install_scripts/GEO/platforms/GPL737.yaml +7 -0
  218. data/install_scripts/GEO/platforms/GPL738.yaml +7 -0
  219. data/install_scripts/GEO/platforms/GPL74.yaml +4 -0
  220. data/install_scripts/GEO/platforms/GPL75.yaml +4 -0
  221. data/install_scripts/GEO/platforms/GPL76.yaml +4 -0
  222. data/install_scripts/GEO/platforms/GPL764.yaml +7 -0
  223. data/install_scripts/GEO/platforms/GPL772.yaml +7 -0
  224. data/install_scripts/GEO/platforms/GPL782.yaml +7 -0
  225. data/install_scripts/GEO/platforms/GPL783.yaml +7 -0
  226. data/install_scripts/GEO/platforms/GPL784.yaml +7 -0
  227. data/install_scripts/GEO/platforms/GPL80.yaml +4 -0
  228. data/install_scripts/GEO/platforms/GPL81.yaml +4 -0
  229. data/install_scripts/GEO/platforms/GPL82.yaml +4 -0
  230. data/install_scripts/GEO/platforms/GPL83.yaml +4 -0
  231. data/install_scripts/GEO/platforms/GPL85.yaml +4 -0
  232. data/install_scripts/GEO/platforms/GPL86.yaml +4 -0
  233. data/install_scripts/GEO/platforms/GPL87.yaml +4 -0
  234. data/install_scripts/GEO/platforms/GPL870.yaml +7 -0
  235. data/install_scripts/GEO/platforms/GPL875.yaml +7 -0
  236. data/install_scripts/GEO/platforms/GPL884.yaml +7 -0
  237. data/install_scripts/GEO/platforms/GPL887.yaml +7 -0
  238. data/install_scripts/GEO/platforms/GPL89.yaml +4 -0
  239. data/install_scripts/GEO/platforms/GPL890.yaml +7 -0
  240. data/install_scripts/GEO/platforms/GPL891.yaml +7 -0
  241. data/install_scripts/GEO/platforms/GPL90.yaml +7 -0
  242. data/install_scripts/GEO/platforms/GPL91.yaml +4 -0
  243. data/install_scripts/GEO/platforms/GPL92.yaml +4 -0
  244. data/install_scripts/GEO/platforms/GPL920.yaml +7 -0
  245. data/install_scripts/GEO/platforms/GPL922.yaml +7 -0
  246. data/install_scripts/GEO/platforms/GPL924.yaml +7 -0
  247. data/install_scripts/GEO/platforms/GPL93.yaml +4 -0
  248. data/install_scripts/GEO/platforms/GPL96.yaml +4 -0
  249. data/install_scripts/GEO/platforms/GPL968.yaml +4 -0
  250. data/install_scripts/GEO/platforms/GPL97.yaml +4 -0
  251. data/install_scripts/GEO/platforms/GPL98.yaml +7 -0
  252. data/install_scripts/GEO/platforms/GPL981.yaml +7 -0
  253. data/install_scripts/GEO/platforms/GPL99.yaml +7 -0
  254. data/install_scripts/GEO/platforms/GPL999.yaml +7 -0
  255. data/install_scripts/GEO/series/GSE10018.yaml +61 -0
  256. data/install_scripts/GEO/series/GSE1002.yaml +135 -0
  257. data/install_scripts/GEO/series/GSE10066.yaml +31 -0
  258. data/install_scripts/GEO/series/GSE10073.yaml +19 -0
  259. data/install_scripts/GEO/series/GSE10091.yaml +15 -0
  260. data/install_scripts/GEO/series/GSE101.yaml +17 -0
  261. data/install_scripts/GEO/series/GSE10100.yaml +15 -0
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  267. data/install_scripts/GEO/series/GSE103.yaml +19 -0
  268. data/install_scripts/GEO/series/GSE104.yaml +19 -0
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  270. data/install_scripts/GEO/series/GSE10521.yaml +56 -0
  271. data/install_scripts/GEO/series/GSE10554.yaml +19 -0
  272. data/install_scripts/GEO/series/GSE1073.yaml +127 -0
  273. data/install_scripts/GEO/series/GSE10860.yaml +25 -0
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  296. data/install_scripts/GEO/series/GSE11983.yaml +15 -0
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  298. data/install_scripts/GEO/series/GSE12055.yaml +109 -0
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  300. data/install_scripts/GEO/series/GSE12104.yaml +10 -0
  301. data/install_scripts/GEO/series/GSE12138.yaml +13 -0
  302. data/install_scripts/GEO/series/GSE12150.yaml +32 -0
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  305. data/install_scripts/GEO/series/GSE1365.yaml +14 -0
  306. data/install_scripts/GEO/series/GSE1404.yaml +596 -0
  307. data/install_scripts/GEO/series/GSE1492.yaml +15 -0
  308. data/install_scripts/GEO/series/GSE15222.yaml +731 -0
  309. data/install_scripts/GEO/series/GSE1553.yaml +23 -0
  310. data/install_scripts/GEO/series/GSE1617.yaml +39 -0
  311. data/install_scripts/GEO/series/GSE1688.yaml +36 -0
  312. data/install_scripts/GEO/series/GSE1693.yaml +60 -0
  313. data/install_scripts/GEO/series/GSE1752.yaml +32 -0
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  319. data/install_scripts/GEO/series/GSE1763.yaml +19 -0
  320. data/install_scripts/GEO/series/GSE1915.yaml +39 -0
  321. data/install_scripts/GEO/series/GSE1927.yaml +14 -0
  322. data/install_scripts/GEO/series/GSE1941.yaml +23 -0
  323. data/install_scripts/GEO/series/GSE1942.yaml +31 -0
  324. data/install_scripts/GEO/series/GSE1944.yaml +58 -0
  325. data/install_scripts/GEO/series/GSE1975.yaml +65 -0
  326. data/install_scripts/GEO/series/GSE20.yaml +24 -0
  327. data/install_scripts/GEO/series/GSE2107.yaml +14 -0
  328. data/install_scripts/GEO/series/GSE2159.yaml +31 -0
  329. data/install_scripts/GEO/series/GSE2246.yaml +157 -0
  330. data/install_scripts/GEO/series/GSE2263.yaml +57 -0
  331. data/install_scripts/GEO/series/GSE2267.yaml +155 -0
  332. data/install_scripts/GEO/series/GSE23.yaml +58 -0
  333. data/install_scripts/GEO/series/GSE2329.yaml +43 -0
  334. data/install_scripts/GEO/series/GSE2330.yaml +55 -0
  335. data/install_scripts/GEO/series/GSE2349.yaml +19 -0
  336. data/install_scripts/GEO/series/GSE2412.yaml +58 -0
  337. data/install_scripts/GEO/series/GSE2419.yaml +27 -0
  338. data/install_scripts/GEO/series/GSE2420.yaml +29 -0
  339. data/install_scripts/GEO/series/GSE2434.yaml +37 -0
  340. data/install_scripts/GEO/series/GSE2526.yaml +23 -0
  341. data/install_scripts/GEO/series/GSE2579.yaml +19 -0
  342. data/install_scripts/GEO/series/GSE2806.yaml +11 -0
  343. data/install_scripts/GEO/series/GSE2831.yaml +35 -0
  344. data/install_scripts/GEO/series/GSE2832.yaml +17 -0
  345. data/install_scripts/GEO/series/GSE29.yaml +16 -0
  346. data/install_scripts/GEO/series/GSE3006.yaml +35 -0
  347. data/install_scripts/GEO/series/GSE3043.yaml +18 -0
  348. data/install_scripts/GEO/series/GSE3122.yaml +12 -0
  349. data/install_scripts/GEO/series/GSE3130.yaml +12 -0
  350. data/install_scripts/GEO/series/GSE3151.yaml +118 -0
  351. data/install_scripts/GEO/series/GSE3160.yaml +31 -0
  352. data/install_scripts/GEO/series/GSE3190.yaml +14 -0
  353. data/install_scripts/GEO/series/GSE3205.yaml +36 -0
  354. data/install_scripts/GEO/series/GSE3206.yaml +23 -0
  355. data/install_scripts/GEO/series/GSE3315.yaml +13 -0
  356. data/install_scripts/GEO/series/GSE3335.yaml +15 -0
  357. data/install_scripts/GEO/series/GSE34.yaml +31 -0
  358. data/install_scripts/GEO/series/GSE3470.yaml +15 -0
  359. data/install_scripts/GEO/series/GSE35.yaml +80 -0
  360. data/install_scripts/GEO/series/GSE3503.yaml +19 -0
  361. data/install_scripts/GEO/series/GSE3683.yaml +83 -0
  362. data/install_scripts/GEO/series/GSE3684.yaml +19 -0
  363. data/install_scripts/GEO/series/GSE3685.yaml +31 -0
  364. data/install_scripts/GEO/series/GSE3686.yaml +63 -0
  365. data/install_scripts/GEO/series/GSE3687.yaml +83 -0
  366. data/install_scripts/GEO/series/GSE3802.yaml +19 -0
  367. data/install_scripts/GEO/series/GSE3803.yaml +19 -0
  368. data/install_scripts/GEO/series/GSE3804.yaml +19 -0
  369. data/install_scripts/GEO/series/GSE3805.yaml +19 -0
  370. data/install_scripts/GEO/series/GSE3813.yaml +9 -0
  371. data/install_scripts/GEO/series/GSE3814.yaml +71 -0
  372. data/install_scripts/GEO/series/GSE3815.yaml +75 -0
  373. data/install_scripts/GEO/series/GSE3817.yaml +13 -0
  374. data/install_scripts/GEO/series/GSE3818.yaml +15 -0
  375. data/install_scripts/GEO/series/GSE3819.yaml +13 -0
  376. data/install_scripts/GEO/series/GSE3820.yaml +61 -0
  377. data/install_scripts/GEO/series/GSE3821.yaml +55 -0
  378. data/install_scripts/GEO/series/GSE3844.yaml +11 -0
  379. data/install_scripts/GEO/series/GSE3853.yaml +31 -0
  380. data/install_scripts/GEO/series/GSE3935.yaml +12 -0
  381. data/install_scripts/GEO/series/GSE3969.yaml +14 -0
  382. data/install_scripts/GEO/series/GSE4049.yaml +80 -0
  383. data/install_scripts/GEO/series/GSE4144.yaml +9 -0
  384. data/install_scripts/GEO/series/GSE4261.yaml +59 -0
  385. data/install_scripts/GEO/series/GSE4295.yaml +63 -0
  386. data/install_scripts/GEO/series/GSE4398.yaml +50 -0
  387. data/install_scripts/GEO/series/GSE4719.yaml +76 -0
  388. data/install_scripts/GEO/series/GSE4720.yaml +78 -0
  389. data/install_scripts/GEO/series/GSE4721.yaml +14 -0
  390. data/install_scripts/GEO/series/GSE4807.yaml +67 -0
  391. data/install_scripts/GEO/series/GSE4826.yaml +39 -0
  392. data/install_scripts/GEO/series/GSE4934.yaml +23 -0
  393. data/install_scripts/GEO/series/GSE5027.yaml +31 -0
  394. data/install_scripts/GEO/series/GSE5070.yaml +25 -0
  395. data/install_scripts/GEO/series/GSE5238.yaml +31 -0
  396. data/install_scripts/GEO/series/GSE5267.yaml +55 -0
  397. data/install_scripts/GEO/series/GSE5281.yaml +492 -0
  398. data/install_scripts/GEO/series/GSE5290.yaml +24 -0
  399. data/install_scripts/GEO/series/GSE5376.yaml +107 -0
  400. data/install_scripts/GEO/series/GSE5575.yaml +13 -0
  401. data/install_scripts/GEO/series/GSE5835.yaml +25 -0
  402. data/install_scripts/GEO/series/GSE5836.yaml +37 -0
  403. data/install_scripts/GEO/series/GSE5837.yaml +37 -0
  404. data/install_scripts/GEO/series/GSE5938.yaml +187 -0
  405. data/install_scripts/GEO/series/GSE600.yaml +29 -0
  406. data/install_scripts/GEO/series/GSE6018.yaml +55 -0
  407. data/install_scripts/GEO/series/GSE6066.yaml +20 -0
  408. data/install_scripts/GEO/series/GSE6067.yaml +31 -0
  409. data/install_scripts/GEO/series/GSE6068.yaml +55 -0
  410. data/install_scripts/GEO/series/GSE6070.yaml +31 -0
  411. data/install_scripts/GEO/series/GSE6071.yaml +30 -0
  412. data/install_scripts/GEO/series/GSE6072.yaml +37 -0
  413. data/install_scripts/GEO/series/GSE6101.yaml +26 -0
  414. data/install_scripts/GEO/series/GSE6111.yaml +20 -0
  415. data/install_scripts/GEO/series/GSE6190.yaml +30 -0
  416. data/install_scripts/GEO/series/GSE6277.yaml +19 -0
  417. data/install_scripts/GEO/series/GSE6331.yaml +51 -0
  418. data/install_scripts/GEO/series/GSE6346.yaml +49 -0
  419. data/install_scripts/GEO/series/GSE6358.yaml +22 -0
  420. data/install_scripts/GEO/series/GSE6405.yaml +36 -0
  421. data/install_scripts/GEO/series/GSE6450.yaml +51 -0
  422. data/install_scripts/GEO/series/GSE6687.yaml +15 -0
  423. data/install_scripts/GEO/series/GSE6705.yaml +19 -0
  424. data/install_scripts/GEO/series/GSE6801.yaml +27 -0
  425. data/install_scripts/GEO/series/GSE6847.yaml +18 -0
  426. data/install_scripts/GEO/series/GSE6870.yaml +23 -0
  427. data/install_scripts/GEO/series/GSE7103.yaml +28 -0
  428. data/install_scripts/GEO/series/GSE7140.yaml +19 -0
  429. data/install_scripts/GEO/series/GSE7188.yaml +23 -0
  430. data/install_scripts/GEO/series/GSE7261.yaml +16 -0
  431. data/install_scripts/GEO/series/GSE7337.yaml +19 -0
  432. data/install_scripts/GEO/series/GSE7338.yaml +19 -0
  433. data/install_scripts/GEO/series/GSE7362.yaml +123 -0
  434. data/install_scripts/GEO/series/GSE7369.yaml +15 -0
  435. data/install_scripts/GEO/series/GSE7525.yaml +33 -0
  436. data/install_scripts/GEO/series/GSE7537.yaml +27 -0
  437. data/install_scripts/GEO/series/GSE7645.yaml +152 -0
  438. data/install_scripts/GEO/series/GSE7660.yaml +41 -0
  439. data/install_scripts/GEO/series/GSE7820.yaml +30 -0
  440. data/install_scripts/GEO/series/GSE79.yaml +32 -0
  441. data/install_scripts/GEO/series/GSE8035.yaml +19 -0
  442. data/install_scripts/GEO/series/GSE8088.yaml +13 -0
  443. data/install_scripts/GEO/series/GSE8089.yaml +19 -0
  444. data/install_scripts/GEO/series/GSE8111.yaml +15 -0
  445. data/install_scripts/GEO/series/GSE8237.yaml +35 -0
  446. data/install_scripts/GEO/series/GSE8326.yaml +37 -0
  447. data/install_scripts/GEO/series/GSE8399.yaml +13 -0
  448. data/install_scripts/GEO/series/GSE850.yaml +15 -0
  449. data/install_scripts/GEO/series/GSE8506.yaml +32 -0
  450. data/install_scripts/GEO/series/GSE8542.yaml +47 -0
  451. data/install_scripts/GEO/series/GSE8558.yaml +19 -0
  452. data/install_scripts/GEO/series/GSE8559.yaml +47 -0
  453. data/install_scripts/GEO/series/GSE8613.yaml +19 -0
  454. data/install_scripts/GEO/series/GSE8629.yaml +18 -0
  455. data/install_scripts/GEO/series/GSE8729.yaml +19 -0
  456. data/install_scripts/GEO/series/GSE8761.yaml +55 -0
  457. data/install_scripts/GEO/series/GSE8765.yaml +15 -0
  458. data/install_scripts/GEO/series/GSE8805.yaml +64 -0
  459. data/install_scripts/GEO/series/GSE8825.yaml +79 -0
  460. data/install_scripts/GEO/series/GSE8895.yaml +31 -0
  461. data/install_scripts/GEO/series/GSE8897.yaml +17 -0
  462. data/install_scripts/GEO/series/GSE8898.yaml +18 -0
  463. data/install_scripts/GEO/series/GSE8900.yaml +43 -0
  464. data/install_scripts/GEO/series/GSE8982.yaml +106 -0
  465. data/install_scripts/GEO/series/GSE920.yaml +20 -0
  466. data/install_scripts/GEO/series/GSE960.yaml +10 -0
  467. data/install_scripts/GEO/series/GSE961.yaml +14 -0
  468. data/install_scripts/GEO/series/GSE962.yaml +20 -0
  469. data/install_scripts/GEO/series/GSE963.yaml +14 -0
  470. data/install_scripts/GEO/series/GSE964.yaml +14 -0
  471. data/install_scripts/GEO/series/GSE965.yaml +14 -0
  472. data/install_scripts/GEO/series/GSE966.yaml +14 -0
  473. data/install_scripts/GEO/series/GSE993.yaml +9 -0
  474. data/lib/MARQ.rb +79 -0
  475. data/lib/MARQ/CustomDS.rb +99 -0
  476. data/lib/MARQ/GEO.rb +588 -0
  477. data/lib/MARQ/ID.rb +144 -0
  478. data/lib/MARQ/MADB.rb +238 -0
  479. data/lib/MARQ/annotations.rb +740 -0
  480. data/lib/MARQ/fdr.rb +177 -0
  481. data/lib/MARQ/main.rb +227 -0
  482. data/lib/MARQ/rankproduct.rb +146 -0
  483. data/lib/MARQ/score.rb +395 -0
  484. data/tasks/install.rake +21 -0
  485. metadata +588 -0
data/LICENSE ADDED
@@ -0,0 +1,20 @@
1
+ Copyright (c) 2009 Miguel Vazquez
2
+
3
+ Permission is hereby granted, free of charge, to any person obtaining
4
+ a copy of this software and associated documentation files (the
5
+ "Software"), to deal in the Software without restriction, including
6
+ without limitation the rights to use, copy, modify, merge, publish,
7
+ distribute, sublicense, and/or sell copies of the Software, and to
8
+ permit persons to whom the Software is furnished to do so, subject to
9
+ the following conditions:
10
+
11
+ The above copyright notice and this permission notice shall be
12
+ included in all copies or substantial portions of the Software.
13
+
14
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
15
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
16
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
17
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
18
+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
19
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
20
+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
data/R/CustomDS.R ADDED
@@ -0,0 +1,80 @@
1
+ CustomDS.process <- function(prefix, cross_platform, conditions, description, two.channel,do.log2 = NULL){
2
+ tryCatch({
3
+
4
+ # Read data
5
+ genes = scan(file=paste(prefix,'codes',sep = "/"), what=character(),sep="\n",quiet=T);
6
+ m = matrix(scan(file=paste(prefix,'values',sep = "/"), sep="\t",quiet=T),length(genes),byrow=T);
7
+ rownames(m) <- genes
8
+
9
+ # Read conditions
10
+ conditions.list = vector();
11
+ names = vector();
12
+ for (file in conditions){
13
+ values = scan(paste(prefix,file,sep="/"),what=character(),sep="\n",quiet=T)
14
+ names = c(names, file)
15
+ conditions.list = cbind(conditions.list, values)
16
+ }
17
+
18
+
19
+
20
+
21
+ # Do log2 if needed
22
+ if (is.null(do.log2)){
23
+ do.log2 = MA.guess.do.log2(m, two.channel)
24
+ }
25
+ if (do.log2){
26
+ m <- log2(m);
27
+ }
28
+ m[is.infinite(m)] = NA; # The log may have created infinite values
29
+
30
+ # Make translations to genes
31
+ if (cross_platform){
32
+ trans = scan(file=paste(prefix,'cross_platform',sep = "/"),what=character(),sep="\n",quiet=T);
33
+ if (!is.null(trans)){
34
+ m <- MA.translate(m, trans);
35
+ }
36
+ }
37
+
38
+ # Once the data is read, change the prefix for cross_platform ids
39
+ if (cross_platform){
40
+ prefix = paste(prefix,'cross_platform', sep="_")
41
+ }
42
+ colnames(conditions.list) <- names;
43
+
44
+ values <- MA.process(m, conditions.list, two.channel);
45
+
46
+ ratios = as.data.frame(values$ratios);
47
+ t = as.data.frame(values$t);
48
+ p.values = as.data.frame(values$p.values);
49
+
50
+
51
+ # Calculate orders from best information
52
+ best = vector();
53
+ names = vector();
54
+ for (name in colnames(ratios)){
55
+ if (sum(colnames(t) == name) > 0){
56
+ best = cbind(best, t[,name]);
57
+ names = c(names, name);
58
+ }else{
59
+ best = cbind(best, ratios[,name]);
60
+ names = c(names, paste(name,'[ratio]', sep=" "));
61
+ }
62
+ }
63
+ rownames(best) <- rownames(ratios);
64
+ orders = as.data.frame(MA.get_order(best));
65
+ colnames(orders) <- names;
66
+
67
+
68
+ if (is.null(values)){
69
+ write(file=paste(prefix,'skip',sep="."), "no suitable samples for analysis" );
70
+ }else{
71
+ MA.save(prefix, orders, ratios, t, p.values, colnames(orders), description);
72
+ }
73
+ },
74
+ error=function(x){
75
+ print("exception caught");
76
+ print(x);
77
+ write(file=paste(prefix,'skip',sep="."), paste("an exception was caught during the analysis.",x,sep="\n") );
78
+ }
79
+ )
80
+ }
data/R/GEO.R ADDED
@@ -0,0 +1,249 @@
1
+ library(Biobase);
2
+ library(GEOquery);
3
+
4
+ GEO.values <- function(data){
5
+ values <- MA.process(data$m, data$conditions, data$two.channel)
6
+
7
+ if (length(values$ratios) == 0){
8
+ return(NULL);
9
+ }else{
10
+ ratios = as.data.frame(values$ratios);
11
+ t = as.data.frame(values$t);
12
+ p.values = as.data.frame(values$p.values);
13
+
14
+
15
+ # Calculate orders from best information
16
+ best = vector();
17
+ names = vector();
18
+ for (name in colnames(ratios)){
19
+ if (sum(colnames(t) == name) > 0){
20
+ best = cbind(best, t[,name]);
21
+ names = c(names, name);
22
+ }else{
23
+ best = cbind(best, ratios[,name]);
24
+ names = c(names, paste(name,'[ratio]', sep=" "));
25
+ }
26
+ }
27
+ rownames(best) <- rownames(ratios)
28
+ orders = as.data.frame(MA.get_order(best));
29
+ colnames(orders) <- names
30
+
31
+ return(list(ratios = ratios, t = t, p.values = p.values, orders = orders));
32
+ }
33
+ }
34
+
35
+
36
+
37
+ GEO.get <- function(name, cachedir = NULL){
38
+ if (is.null(cachedir)){
39
+ object <- getGEO(name);
40
+ }else{
41
+ filename = dir(cachedir,pattern= paste(name, 'soft', sep='.'))[1]
42
+ if (is.na(filename)){
43
+ object <- getGEO(name, destdir=cachedir);
44
+ }else{
45
+ object <- getGEO(name, filename = paste(cachedir,filename,sep="/"));
46
+ }
47
+ }
48
+
49
+ object
50
+ }
51
+
52
+ # Parses phenotype data structure to determine the conditions
53
+ GEO.find_conditions <- function(ph) {
54
+ # Find conditions
55
+ labels = varLabels(ph);
56
+
57
+ # Removed not usefull
58
+ labels = labels[-grep('sample|description|individual|none',labels)]
59
+
60
+ # Find labels with replicates
61
+
62
+ labels
63
+ }
64
+
65
+ GEO.GDS.data <- function(name, id.field = NULL, translation.file = NULL, cachedir = NULL){
66
+
67
+ gds = GEO.get(name, cachedir);
68
+
69
+ gpl_name = Meta(gds)$platform
70
+ gpl = GEO.get(gpl_name, cachedir);
71
+ description = paste(Meta(gds)$title, Meta(gds)$description, sep="\n--\n")
72
+
73
+
74
+ two.channel <- attr(gds,'header')$channel_count == '2'
75
+ value.type <- attr(gds,'header')$value_type
76
+ if (length(grep('log',value.type)) == 0){
77
+ do.log2 = TRUE;
78
+ }else{
79
+ do.log2 = FALSE;
80
+ }
81
+ eSet <- GDS2eSet(gds, GPL=gpl, do.log2 = do.log2 );
82
+
83
+ ph = phenoData(eSet)
84
+ conditions = sapply(GEO.find_conditions(ph), function(condition){ph[[condition]]});
85
+
86
+ m = exprs(eSet)
87
+
88
+ trans = NULL
89
+ if (!is.null(id.field)){
90
+ trans = featureData(eSet)[[id.field]];
91
+ }
92
+ if (!is.null(translation.file)){
93
+ trans = scan(file=translation.file,what=character(),sep="\n",quiet=T);
94
+ }
95
+
96
+ if (!is.null(trans)){
97
+ m <- MA.translate(m, trans);
98
+ }
99
+
100
+
101
+
102
+ return (list(conditions = conditions, m = m, two.channel = two.channel, description = description))
103
+ }
104
+
105
+
106
+ GEO.GDS.process <- function(name, prefix, id.field = NULL, translation.file = NULL,cachedir=NULL){
107
+ tryCatch(
108
+ {
109
+ gds.data = GEO.GDS.data(name, id.field, translation.file, cachedir)
110
+ values = GEO.values(gds.data)
111
+ if (is.null(values)){
112
+ write(file=paste(prefix,'skip',sep="."), "No suitable samples for analysis" );
113
+ }else{
114
+ MA.save(prefix, values$orders, values$ratios, values$t, values$p.values, colnames(values$orders), gds.data$description);
115
+ }
116
+ }
117
+ ,
118
+ error=function(x){
119
+ print("Exception caught");
120
+ print(x);
121
+ write(file=paste(prefix,'skip',sep="."), paste("An exception was caught during the analysis.",x,sep="\n") );
122
+ }
123
+ )
124
+ }
125
+
126
+
127
+
128
+
129
+ GEO.GSE.data <- function(gsms, conditions, do.log2 = NULL, translation.file = NULL, use.fields = NULL, cachedir = NULL){
130
+
131
+ c = sapply(conditions,function(x){x});
132
+ colnames(c) <- names(conditions);
133
+ conditions = c;
134
+
135
+ # Get gene names
136
+ gene.names = vector();
137
+ for(name in gsms){
138
+ gsm = GEO.get(name, cachedir);
139
+ data = attr(dataTable(gsm),'table');
140
+ if (!is.null(use.fields)){
141
+ gsm.names = levels(factor(data[,use.fields[name]]))
142
+ }else{
143
+ gsm.names = levels(factor(data[,1]))
144
+ }
145
+ gene.names <- c(gene.names, gsm.names)
146
+ }
147
+
148
+ gene.names= sort(unique((gene.names)));
149
+ gene.names = gene.names[gene.names != ""];
150
+
151
+
152
+ # Merge Arrays
153
+ init <- rep(NA,length(gene.names))
154
+ names(init) <- gene.names;
155
+ m <- NULL;
156
+ for(name in gsms){
157
+ gsm = GEO.get(name, cachedir);
158
+ two.channel <- attr(gsm,'header')$channel_count == '2';
159
+ data = attr(dataTable(gsm),'table')
160
+ values = as.numeric(data[,"VALUE"])
161
+
162
+ # Merge duplicates
163
+
164
+
165
+ if (!is.null(use.fields)){
166
+ names = factor(data[,use.fields[name]])
167
+ }else{
168
+ names = factor(data[,1])
169
+ }
170
+
171
+ values = tapply(values, factor(names), mean, na.rm = T)
172
+ n <- names(values)
173
+ values = as.vector(values)
174
+ names(values) <- n
175
+
176
+ if (is.null(m)){
177
+ m = init
178
+ m[names(values)] = values
179
+ }else{
180
+ new = init
181
+ new[names(values)] = values;
182
+ m = cbind(m, new)
183
+ }
184
+ }
185
+ colnames(m) <- as.list(gsms);
186
+
187
+
188
+
189
+ if (is.null(m)){
190
+ return(NULL);
191
+ }
192
+
193
+ trans = NULL
194
+ if (!is.null(translation.file)){
195
+ trans = read.table(file=translation.file, sep="\t",header=F)[,1];
196
+ }
197
+ if (!is.null(trans)){
198
+ m <- MA.translate(m, trans);
199
+ }
200
+
201
+ if(is.null(do.log2)){
202
+ do.log2 = MA.guess.do.log2(m, two.channel);
203
+ }
204
+
205
+ if (do.log2){
206
+ m <- log2(m);
207
+ }
208
+
209
+ # The log may have created infinite values
210
+ m[is.infinite(m)] = NA
211
+
212
+ return (list(conditions = conditions, m = m, two.channel = two.channel))
213
+ }
214
+
215
+ GEO.GSE.process <- function(gsms, conditions, prefix, do.log2 = NULL, translation.file = NULL, use.field = NULL, title = NULL, description = NULL,cachedir=NULL){
216
+ tryCatch(
217
+ {
218
+ gse.data = GEO.GSE.data(gsms, conditions, do.log2, translation.file, use.field, cachedir)
219
+ values = GEO.values(gse.data)
220
+ full_desc = paste(title, description, sep="\n--\n")
221
+ if (is.null(values)){
222
+ write(file=paste(prefix,'skip',sep="."), "No suitable samples for analysis" );
223
+ }else{
224
+ MA.save(prefix, values$orders, values$ratios, values$t, values$p.values, colnames(values$orders), full_desc );
225
+ }
226
+ }
227
+ ,
228
+ error=function(x){
229
+ print("Exception caught");
230
+ print(x);
231
+ write(file=paste(prefix,'skip',sep="."), paste("An exception was caught during the analysis.",x,sep="\n") );
232
+ }
233
+ )
234
+
235
+ }
236
+
237
+
238
+ GEO.GPL.process <- function(name, prefix, id.field = NULL, cachedir = NULL){
239
+ gpl = GEO.get(name, cachedir);
240
+ if (is.null(id.field)){
241
+ ids <- Table(gpl)$ID;
242
+ }else{
243
+ ids <- Table(gpl)[[id.field]];
244
+ }
245
+
246
+ write.table(file=paste(prefix,'codes',sep="."), ids, sep="\t", row.names=F, col.names=F, quote=F);
247
+ }
248
+
249
+
data/R/MA.R ADDED
@@ -0,0 +1,359 @@
1
+ library(limma)
2
+
3
+ MA.get_order <- function(values){
4
+ orders = values;
5
+ orders[,] = NA;
6
+
7
+ for (i in 1:dim(values)[2]){
8
+ positions = names(sort(values[,i],decreasing=T))
9
+
10
+ orders[,i] = NA
11
+ orders[positions,i] = 1:length(positions)
12
+ }
13
+ orders
14
+ }
15
+
16
+ MA.guess.do.log2 <- function(m, two.channel){
17
+ if (two.channel){
18
+ return (sum(m < 0, na.rm = TRUE) == 0);
19
+ }else{
20
+ return (max(m, na.rm = TRUE) > 100);
21
+ }
22
+ }
23
+
24
+ MA.translate <- function(m, trans){
25
+ trans[trans==""] = NA;
26
+ trans[trans=="NO MATCH"] = NA;
27
+
28
+ missing = length(trans) - dim(m)[1];
29
+
30
+ # If extra genes
31
+ if (missing < 0){
32
+ trans = c(trans,rep(NA, - missing))
33
+ missing = 0;
34
+ }
35
+ n = apply(m,2,function(x){
36
+
37
+ # Complete data with missing genes
38
+ x.complete = c(x,rep(NA, missing));
39
+ tapply(x.complete, factor(trans), median)
40
+ });
41
+ n[sort(rownames(n),index.return=T)$ix,]
42
+ }
43
+
44
+ # Conditions
45
+
46
+ MA.conditions.has_control <- function(x){
47
+ keywords = c('none', 'control', 'normal', 'wild', 'baseline', 'untreat', 'uninfected', 'universal', 'reference', 'vehicle', 'w.t.','wt');
48
+ for(keyword in keywords){
49
+ control = grep(keyword, x, ignore.case = TRUE);
50
+ if (any(control)){
51
+ return(x[control[1]]);
52
+ }
53
+ }
54
+ return(NULL)
55
+ }
56
+
57
+ MA.condition.values <- function(values){
58
+ control = MA.conditions.has_control(values);
59
+
60
+ values.factor = factor(values);
61
+ values.levels = levels(values.factor);
62
+
63
+ # If there is a control state remove it from sorting
64
+ if (!is.null(control))
65
+ values.levels = values.levels[values.levels != control];
66
+
67
+
68
+ # Use numeric sort if they all have numbers
69
+ if (length(grep('^ *[0-9]+',values.levels,perl=TRUE)) == length(values.levels)){
70
+ ix = sort(as.numeric(sub('^ *([0-9]+).*',"\\1",values.levels)), decreasing = T, index.return = TRUE)$ix
71
+ }else{
72
+ ix = sort(values.levels, decreasing = T, index.return = TRUE)$ix
73
+ }
74
+
75
+ return(list(values = values.levels[ix], control = control));
76
+ }
77
+
78
+
79
+ #########################################################################
80
+ # Model processing
81
+
82
+ # Ratio
83
+ MA.ratio.two_channel <- function(m, conditions, main){
84
+ main = m[,conditions==main];
85
+ if (!is.null(dim(main))){
86
+ main = apply(main, 1 ,function(x){mean(x, na.rm = TRUE)});
87
+ }
88
+ return(main);
89
+ }
90
+
91
+ MA.ratio.contrast <- function(m, conditions, main, contrast){
92
+ main = m[,conditions==main];
93
+ if (!is.null(dim(main))){
94
+ main = apply(main, 1 ,function(x){mean(x, na.rm = TRUE)});
95
+ }
96
+
97
+ contrast = m[,conditions==contrast];
98
+ if (!is.null(dim(contrast))){
99
+ contrast = apply(contrast, 1 ,function(x){mean(x, na.rm = TRUE)});
100
+ }
101
+
102
+ return (main - contrast);
103
+ }
104
+
105
+
106
+ # Limma
107
+
108
+ MA.limma.two_channel <- function(m, conditions, main){
109
+ if (sum(conditions == main) < 3){
110
+ return(NULL);
111
+ }
112
+
113
+ design = rep(0,dim(m)[2]);
114
+ design[conditions == main] = 1;
115
+
116
+ # We need to subset the columns because of a problem with NA values. This
117
+ # might affect eBayes variance estimations, thats my guess anyway...
118
+
119
+ fit <- lmFit(m[,design == 1],rep(1, sum(design)));
120
+
121
+ tryCatch({
122
+ fit <- eBayes(fit);
123
+ sign = fit$t < 0;
124
+ sign[is.na(sign)] = FALSE;
125
+ fit$p.value[sign] = - fit$p.value[sign];
126
+ return(list(t= fit$t, p.values= fit$p.value));
127
+ }, error=function(x){
128
+ print("Exception caught in eBayes");
129
+ print(x);
130
+ })
131
+
132
+ return(NULL);
133
+ }
134
+
135
+ MA.limma.contrast <- function(m, conditions, main, contrast){
136
+ if (sum(conditions == main) + sum(conditions == contrast) < 3){
137
+ return(NULL);
138
+ }
139
+ m = cbind(m[,conditions == main],m[,conditions == contrast])
140
+
141
+ design = cbind(rep(1,dim(m)[2]), rep(0,dim(m)[2]));
142
+ colnames(design) <-c('intercept', 'main');
143
+ design[1:sum(conditions==main),2] = 1;
144
+
145
+
146
+ fit <- lmFit(m,design);
147
+ tryCatch({
148
+ fit <- eBayes(fit);
149
+ sign = fit$t[,2] < 0;
150
+ sign[is.na(sign)] = FALSE;
151
+ fit$p.value[sign,2] = - fit$p.value[sign,2]
152
+ return(list(t= fit$t[,2], p.values= fit$p.value[,2] ));
153
+ }, error=function(x){
154
+ print("Exception caught in eBayes");
155
+ print(x);
156
+ })
157
+
158
+ return(NULL);
159
+ }
160
+
161
+
162
+ #########################################################################
163
+ # Process conditions
164
+
165
+ MA.process_conditions.contrasts <- function(m, conditions, two.channel){
166
+ max_levels = 10;
167
+ max_levels_control = 1;
168
+
169
+
170
+ values = MA.condition.values(conditions);
171
+
172
+
173
+ ratios = vector();
174
+ t = vector();
175
+ p.values = vector();
176
+
177
+ ratio_names = vector();
178
+ t_names = vector();
179
+
180
+ if (!is.null(values$control)){
181
+ contrast = values$control;
182
+ for (main in values$values){
183
+ name = paste(main, contrast, sep = " <=> ")
184
+
185
+ ratio = MA.ratio.contrast(m, conditions, main, contrast);
186
+ ratio_names = c(ratio_names, name);
187
+ ratios = cbind(ratios, ratio);
188
+
189
+ res = MA.limma.contrast(m, conditions, main, contrast);
190
+ if (!is.null(res)){
191
+ t_names = c(t_names, name);
192
+ t = cbind(t, res$t);
193
+ p.values = cbind(p.values, res$p.values);
194
+ }
195
+ }
196
+ }
197
+
198
+
199
+ if (length(values$values) <= max_levels_control || (is.null(values$control) && !two.channel && length(values$values) <= max_levels )){
200
+
201
+ remaining = values$values;
202
+ for (main in values$values){
203
+ remaining = remaining[remaining != main];
204
+ for (contrast in remaining){
205
+ name = paste(main, contrast, sep = " <=> ");
206
+
207
+ ratio = MA.ratio.contrast(m, conditions, main, contrast);
208
+ ratio_names = c(ratio_names, name);
209
+ ratios = cbind(ratios, ratio);
210
+
211
+ res = MA.limma.contrast(m, conditions, main, contrast);
212
+ if (!is.null(res)){
213
+ t_names = c(t_names, name);
214
+ t = cbind(t, res$t);
215
+ p.values = cbind(p.values, res$p.values);
216
+ }
217
+ }
218
+ }
219
+ }
220
+
221
+
222
+ if (length(ratio_names) != 0){
223
+ colnames(ratios) <- ratio_names
224
+ }
225
+
226
+ if (length(t_names) != 0){
227
+ colnames(t) <- t_names
228
+ colnames(p.values) <- t_names
229
+ }
230
+
231
+ return(list(ratios = ratios, t=t, p.values = p.values));
232
+ }
233
+
234
+ MA.process_conditions.two_channel <- function(m, conditions){
235
+ values = MA.condition.values(conditions);
236
+
237
+ all_values = values$values
238
+ if (!is.null(values$control)){
239
+ all_values = c(all_values, values$control);
240
+ }
241
+
242
+
243
+ ratios = vector();
244
+ t = vector();
245
+ p.values = vector();
246
+
247
+ ratio_names = vector();
248
+ t_names = vector();
249
+
250
+
251
+ for (main in all_values){
252
+ name = main;
253
+
254
+ ratio = MA.ratio.two_channel(m, conditions, main);
255
+ ratio_names = c(ratio_names, name);
256
+ ratios = cbind(ratios, ratio);
257
+
258
+ res = MA.limma.two_channel(m, conditions, main);
259
+ if (!is.null(res)){
260
+ t_names = c(t_names, name);
261
+ t = cbind(t, res$t);
262
+ p.values = cbind(p.values, res$p.values);
263
+ }
264
+ }
265
+
266
+ if (length(ratio_names) != 0){
267
+ colnames(ratios) <- ratio_names
268
+ }
269
+
270
+ if (length(t_names) != 0){
271
+ colnames(t) <- t_names
272
+ colnames(p.values) <- t_names
273
+ }
274
+
275
+ return(list(ratios = ratios, t=t, p.values = p.values));
276
+ }
277
+
278
+
279
+
280
+ # Process microarray matrix
281
+
282
+ MA.process <- function(m, conditions_list, two.channel = FALSE){
283
+
284
+ ratios = vector();
285
+ t = vector();
286
+ p.values = vector();
287
+
288
+ for(type in colnames(conditions_list)){
289
+ conditions = conditions_list[,type]
290
+
291
+ if (two.channel){
292
+ res = MA.process_conditions.two_channel(m, conditions);
293
+ if (length(res$ratios) != 0){ colnames(res$ratios) <- sapply(colnames(res$ratios),function(x){paste(type,x,sep=": ")}); ratios = cbind(ratios,res$ratios);}
294
+ if (length(res$t) != 0){ colnames(res$t) <- sapply(colnames(res$t),function(x){paste(type,x,sep=": ")}); t = cbind(t,res$t);}
295
+ if (length(res$p.values) != 0){ colnames(res$p.values) <- sapply(colnames(res$p.values),function(x){paste(type,x,sep=": ")}); p.values = cbind(p.values,res$p.values);}
296
+ }
297
+
298
+ res = MA.process_conditions.contrasts(m, conditions, two.channel);
299
+ if (length(res$ratios) != 0){ colnames(res$ratios) <- sapply(colnames(res$ratios),function(x){paste(type,x,sep=": ")}); ratios = cbind(ratios,res$ratios);}
300
+ if (length(res$t) != 0){ colnames(res$t) <- sapply(colnames(res$t),function(x){paste(type,x,sep=": ")}); t = cbind(t,res$t);}
301
+ if (length(res$p.values) != 0){ colnames(res$p.values) <- sapply(colnames(res$p.values),function(x){paste(type,x,sep=": ")}); p.values = cbind(p.values,res$p.values);}
302
+ }
303
+
304
+ return(list(ratios = ratios, t=t, p.values = p.values));
305
+ }
306
+
307
+
308
+ MA.save <- function(prefix, orders, ratios, t , p.values, experiments, description = NULL) {
309
+ if (is.null(orders)){
310
+ write(file=paste(prefix,'skip',sep="."), "No suitable samples for analysis" );
311
+ } else {
312
+ write.table(file=paste(prefix,'orders',sep="."), orders, sep="\t", row.names=F, col.names=F, quote=F);
313
+ write.table(file=paste(prefix,'codes',sep="."), rownames(orders), sep="\t", row.names=F, col.names=F, quote=F);
314
+ write.table(file=paste(prefix,'logratios',sep="."), ratios, sep="\t", row.names=F, col.names=F, quote=F);
315
+ write.table(file=paste(prefix,'t',sep="."), t, sep="\t", row.names=F, col.names=F, quote=F);
316
+ write.table(file=paste(prefix,'pvalues',sep="."), p.values, sep="\t", row.names=F, col.names=F, quote=F);
317
+ write.table(file=paste(prefix,'experiments',sep="."), experiments, sep="\t", row.names=F, col.names=F, quote=F);
318
+
319
+ write(file=paste(prefix,'description',sep="."), description)
320
+ }
321
+ }
322
+
323
+ MA.load <- function(prefix, orders = TRUE, logratios = TRUE, t = TRUE, p.values = TRUE){
324
+ data = list();
325
+ genes <- scan(file=paste(prefix,'codes',sep="."),sep="\n",quiet=T,what=character());
326
+ experiments <- scan(file=paste(prefix,'experiments',sep="."),sep="\n",quiet=T,what=character());
327
+
328
+ experiments.no.ratio = experiments[- grep('ratio', experiments)];
329
+
330
+ if (orders){
331
+ orders <- read.table(file=paste(prefix,'orders',sep="."),sep="\t");
332
+ rownames(orders) <- genes;
333
+ colnames(orders) <- experiments;
334
+ data$orders=orders;
335
+ }
336
+ if (logratios){
337
+ logratios <- read.table(file=paste(prefix,'logratios',sep="."),sep="\t");
338
+ rownames(logratios) <- genes;
339
+ colnames(logratios) <- experiments;
340
+ data$logratios=logratios;
341
+ }
342
+ if (t){
343
+ t <- read.table(file=paste(prefix,'t',sep="."),sep="\t");
344
+ rownames(t) <- genes;
345
+ colnames(t) <- experiments.no.ratio;
346
+ data$t=t;
347
+ }
348
+ if (p.values){
349
+ p.values <- read.table(file=paste(prefix,'pvalues',sep="."),sep="\t");
350
+ rownames(p.values) <- genes;
351
+ colnames(p.values) <- experiments.no.ratio;
352
+ data$p.values=p.values;
353
+ }
354
+
355
+
356
+ return(data);
357
+
358
+
359
+ }