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6
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1 str(LC)
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2 List of 4
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3 $ PeakTable :'data.frame': 1828 obs. of 12 variables:
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4 ..$ ChemSpiderID : chr [1:1828] "" "" "" "" ...
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5 ..$ compound : chr [1:1828] "" "" "" "" ...
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6 ..$ pcgroup : num [1:1828] 187 226 226 226 226 226 226 306 154 154 ...
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7 ..$ adduct : chr [1:1828] "" "" "" "" ...
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8 ..$ isotopes : chr [1:1828] "" "" "" "" ...
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9 ..$ mz : num [1:1828] 253 233 214 215 298 ...
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10 ..$ rt : num [1:1828] 1.27 1.57 1.59 1.59 1.59 ...
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11 ..$ CLASS2 : num [1:1828] 2 2 2 2 2 2 2 2 2 2 ...
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12 ..$ STDmix_GC_01 : num [1:1828] 0 0 0 0 0 0 0 0 0 0 ...
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13 ..$ STDmix_GC_02 : num [1:1828] 0 0 0 0 0 0 0 0 0 0 ...
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14 ..$ STDmix_RP_pos01: num [1:1828] 144.5 32.6 58.5 38.4 152.3 ...
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15 ..$ STDmix_RP_pos02: num [1:1828] 343.4 54.5 79.1 64.9 210.8 ...
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16 $ xset :Formal class 'xsAnnotate' [package "CAMERA"] with 15 slots
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17 .. ..@ groupInfo : num [1:1828, 1:13] 30.2 30.5 31.4 32.4 33.4 ...
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18 .. .. ..- attr(*, "dimnames")=List of 2
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19 .. .. .. ..$ : NULL
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20 .. .. .. ..$ : chr [1:13] "mz", "mzmin", "mzmax", "rt", "rtmin", "rtmax", "npeaks", "CLASS1", "CLASS2", "STDmix_GC_01", "STDmix_GC_02", "STDmix_RP_pos01", "STDmix_RP_pos02"
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21
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22 and groups() function:
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23 "mzmed", "mzmin", "mzmax", "rtmed", "rtmin", "rtmax", "npeaks", "CLASS1", "CLASS2"
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24
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25 .. ..@ pspectra :List of 340
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26 .. .. ..$ : num [1:12] 2 4 5 10 11 13 14 15 16 38 ...
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27 .. .. ..$ : num [1:11] 3 12 45 76 99 ...
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28 .. .. ..$ : num [1:15] 7 8 9 113 162 ...
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29 .. .. ..$ : Named num 1
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30 .. .. .. ..- attr(*, "names")= chr ""
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31 .. .. ..$ : num [1:5] 6 150 473 478 802
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32 .. .. ..$ : num [1:5] 18 28 40 64 85
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33 .. .. ..$ : num [1:5] 89 528 533 596 872
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34 .. .. ..$ : num [1:2] 57 197
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35 .. .. ..$ : num [1:3] 174 708 841
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36 .. .. ..$ : Named num 23
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37 .. .. .. ..- attr(*, "names")= chr ""
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38 .. .. ..$ : num [1:4] 21 34 496 1497
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39 .. .. ..$ : num [1:3] 29 30 44
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40 .. .. ..$ : num [1:5] 283 423 452 486 527
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41 .. .. ..$ : num [1:6] 93 126 251 296 349 406
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42 .. .. ..$ : num [1:3] 301 479 664
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43 .. .. ..$ : num [1:5] 47 105 111 191 237
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44 .. .. ..$ : num [1:5] 185 562 683 923 1548
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45 .. .. ..$ : num [1:2] 469 809
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46 .. .. ..$ : num [1:9] 24 146 548 550 1009 ...
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47 .. .. ..$ : num [1:33] 65 72 134 139 196 200 235 299 355 361 ...
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48 .. .. ..$ : num [1:2] 135 234
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49 .. .. ..$ : num [1:4] 95 326 330 465
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50 .. .. ..$ : num [1:2] 384 699
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51 .. .. ..$ : Named num 388
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52 .. .. .. ..- attr(*, "names")= chr ""
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53 .. .. ..$ : Named num 249
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54 .. .. .. ..- attr(*, "names")= chr ""
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55 .. .. ..$ : num [1:4] 425 485 636 698
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56 .. .. ..$ : Named num 482
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57 .. .. .. ..- attr(*, "names")= chr ""
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58 .. .. ..$ : num [1:2] 310 429
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59 .. .. ..$ : num [1:97] 33 51 67 96 103 106 114 129 136 140 ...
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60 .. .. ..$ : Named num 436
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61 .. .. .. ..- attr(*, "names")= chr ""
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62 .. .. ..$ : num [1:3] 583 790 1029
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63 .. .. ..$ : Named num 593
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64 .. .. .. ..- attr(*, "names")= chr ""
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65 .. .. ..$ : num [1:2] 558 745
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66 .. .. ..$ : Named num 543
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67 .. .. .. ..- attr(*, "names")= chr ""
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68 .. .. ..$ : num [1:44] 43 60 101 121 124 179 211 214 257 263 ...
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69 .. .. ..$ : num [1:2] 243 941
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70 .. .. ..$ : num [1:4] 657 996 1286 1344
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71 .. .. ..$ : num [1:21] 145 195 199 217 230 268 271 279 665 743 ...
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72 .. .. ..$ : Named num 836
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73 .. .. .. ..- attr(*, "names")= chr ""
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74 .. .. ..$ : Named num 694
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75 .. .. .. ..- attr(*, "names")= chr ""
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76 .. .. ..$ : Named num 578
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77 .. .. .. ..- attr(*, "names")= chr ""
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78 .. .. ..$ : Named num 612
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79 .. .. .. ..- attr(*, "names")= chr ""
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80 .. .. ..$ : Named num 684
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81 .. .. .. ..- attr(*, "names")= chr ""
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82 .. .. ..$ : num [1:18] 31 163 194 395 441 ...
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83 .. .. ..$ : num [1:2] 79 282
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84 .. .. ..$ : Named num 297
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85 .. .. .. ..- attr(*, "names")= chr ""
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86 .. .. ..$ : num [1:10] 167 169 281 284 750 ...
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87 .. .. ..$ : num [1:30] 165 796 812 821 829 ...
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88 .. .. ..$ : num [1:4] 112 566 733 1552
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89 .. .. ..$ : num [1:33] 42 63 68 90 92 102 125 130 133 137 ...
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90 .. .. ..$ : num [1:14] 183 188 435 960 1036 ...
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91 .. .. ..$ : Named num 763
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92 .. .. .. ..- attr(*, "names")= chr ""
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93 .. .. ..$ : Named num 704
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94 .. .. .. ..- attr(*, "names")= chr ""
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95 .. .. ..$ : num [1:2] 693 797
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96 .. .. ..$ : Named num 643
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97 .. .. .. ..- attr(*, "names")= chr ""
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98 .. .. ..$ : num [1:45] 62 100 115 128 132 178 327 366 430 492 ...
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99 .. .. ..$ : Named num 838
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100 .. .. .. ..- attr(*, "names")= chr ""
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101 .. .. ..$ : Named num 653
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102 .. .. .. ..- attr(*, "names")= chr ""
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103 .. .. ..$ : num [1:9] 182 186 1035 1040 1045 ...
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104 .. .. ..$ : Named num 250
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105 .. .. .. ..- attr(*, "names")= chr ""
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106 .. .. ..$ : num [1:2] 144 935
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107 .. .. ..$ : num [1:3] 32 1259 1394
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108 .. .. ..$ : Named num 77
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109 .. .. .. ..- attr(*, "names")= chr ""
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110 .. .. ..$ : num [1:27] 19 46 49 107 110 157 159 233 265 314 ...
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111 .. .. ..$ : num [1:4] 253 410 777 991
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112 .. .. ..$ : Named num 1031
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113 .. .. .. ..- attr(*, "names")= chr ""
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114 .. .. ..$ : Named num 978
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115 .. .. .. ..- attr(*, "names")= chr ""
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116 .. .. ..$ : num [1:22] 887 894 1023 1028 1037 ...
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117 .. .. ..$ : num [1:5] 258 312 1669 1670 1694
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118 .. .. ..$ : num [1:19] 319 730 735 888 895 ...
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119 .. .. ..$ : num [1:22] 55 164 541 617 649 656 661 668 753 766 ...
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120 .. .. ..$ : num [1:7] 513 545 770 773 1080 ...
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121 .. .. ..$ : num [1:4] 70 295 634 1665
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122 .. .. ..$ : num [1:3] 625 1447 1453
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123 .. .. ..$ : Named num 287
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124 .. .. .. ..- attr(*, "names")= chr ""
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125 .. .. ..$ : num [1:2] 964 970
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126 .. .. ..$ : num [1:153] 20 22 36 37 39 53 56 58 59 61 ...
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127 .. .. ..$ : num [1:9] 317 323 420 886 1022 ...
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128 .. .. ..$ : Named num 149
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129 .. .. .. ..- attr(*, "names")= chr ""
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130 .. .. ..$ : num [1:6] 487 549 609 623 728 ...
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131 .. .. ..$ : num [1:6] 315 476 1265 1272 1634 ...
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132 .. .. ..$ : num [1:5] 378 383 495 734 1063
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133 .. .. ..$ : num [1:10] 645 818 823 914 919 ...
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134 .. .. ..$ : num [1:7] 815 1388 1457 1539 1555 ...
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135 .. .. ..$ : Named num 1019
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136 .. .. .. ..- attr(*, "names")= chr ""
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137 .. .. ..$ : num [1:6] 391 398 491 742 982 ...
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138 .. .. ..$ : Named num 546
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139 .. .. .. ..- attr(*, "names")= chr ""
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140 .. .. ..$ : num [1:12] 794 804 811 820 828 ...
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141 .. .. ..$ : num [1:24] 1089 1475 1481 1484 1491 ...
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142 .. .. ..$ : num [1:2] 148 151
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143 .. .. ..$ : num [1:33] 74 104 108 147 181 189 224 232 260 298 ...
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144 .. .. ..$ : num [1:17] 293 332 394 447 449 552 619 622 680 805 ...
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145 .. .. ..$ : Named num 309
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146 .. .. .. ..- attr(*, "names")= chr ""
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147 .. .. ..$ : Named num 207
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148 .. .. .. ..- attr(*, "names")= chr ""
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149 .. .. ..$ : Named num 584
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150 .. .. .. ..- attr(*, "names")= chr ""
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151 .. .. ..$ : num [1:2] 637 865
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152 .. .. ..$ : Named num 143
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153 .. .. .. ..- attr(*, "names")= chr ""
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154 .. .. ..$ : num [1:18] 1737 1738 1741 1757 1758 ...
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155 .. .. ..$ : num [1:29] 261 352 360 363 402 408 416 419 456 507 ...
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156 .. .. .. [list output truncated]
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157 .. ..@ psSamples : int [1:340] 1 1 1 2 2 2 2 1 2 1 ...
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158 .. ..@ isotopes :List of 1828
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159 .. .. ..$ : NULL
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160 .. .. ..$ : NULL
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161 .. .. ..$ : NULL
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162 .. .. ..$ : NULL
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163 .. .. ..$ : NULL
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164 .. .. ..$ : NULL
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165 .. .. ..$ : NULL
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166 .. .. ..$ : NULL
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167 .. .. ..$ : NULL
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168 .. .. ..$ : NULL
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169 .. .. ..$ : NULL
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170 .. .. ..$ : NULL
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171 .. .. ..$ : NULL
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172 .. .. ..$ :List of 4
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173 .. .. .. ..$ y : num 1
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174 .. .. .. ..$ iso : num 0
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175 .. .. .. ..$ charge: Named num 1
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176 .. .. .. .. ..- attr(*, "names")= chr "charge"
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177 .. .. .. ..$ val : Named num 0
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178 .. .. .. .. ..- attr(*, "names")= chr "intrinsic"
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179 .. .. ..$ :List of 4
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180 .. .. .. ..$ y : num 1
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181 .. .. .. ..$ iso : Named num 1
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182 .. .. .. .. ..- attr(*, "names")= chr "iso"
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183 .. .. .. ..$ charge: Named num 1
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184 .. .. .. .. ..- attr(*, "names")= chr "charge"
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185 .. .. .. ..$ val : Named num 0
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186 .. .. .. .. ..- attr(*, "names")= chr "intrinsic"
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187 .. .. ..$ : NULL
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188 .. .. ..$ : NULL
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189 .. .. ..$ : NULL
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190 .. .. ..$ : NULL
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191 .. .. ..$ : NULL
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192 .. .. ..$ : NULL
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193 .. .. ..$ : NULL
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194 .. .. ..$ : NULL
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195 .. .. ..$ : NULL
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196 .. .. ..$ : NULL
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197 .. .. ..$ : NULL
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198 .. .. ..$ : NULL
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199 .. .. ..$ : NULL
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200 .. .. ..$ : NULL
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201 .. .. ..$ : NULL
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202 .. .. ..$ : NULL
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203 .. .. ..$ : NULL
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204 .. .. ..$ : NULL
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205 .. .. ..$ : NULL
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206 .. .. ..$ : NULL
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207 .. .. ..$ : NULL
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208 .. .. ..$ : NULL
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209 .. .. ..$ : NULL
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210 .. .. ..$ : NULL
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211 .. .. ..$ : NULL
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212 .. .. ..$ : NULL
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213 .. .. ..$ : NULL
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214 .. .. ..$ : NULL
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215 .. .. ..$ : NULL
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216 .. .. ..$ : NULL
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217 .. .. ..$ : NULL
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218 .. .. ..$ : NULL
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219 .. .. ..$ : NULL
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220 .. .. ..$ : NULL
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221 .. .. ..$ : NULL
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222 .. .. ..$ : NULL
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223 .. .. ..$ : NULL
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224 .. .. ..$ : NULL
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225 .. .. ..$ : NULL
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226 .. .. ..$ : NULL
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227 .. .. ..$ : NULL
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228 .. .. ..$ : NULL
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229 .. .. ..$ : NULL
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230 .. .. ..$ : NULL
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231 .. .. ..$ : NULL
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232 .. .. ..$ : NULL
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233 .. .. ..$ : NULL
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234 .. .. ..$ : NULL
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235 .. .. ..$ : NULL
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236 .. .. ..$ : NULL
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237 .. .. ..$ : NULL
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238 .. .. ..$ : NULL
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239 .. .. ..$ : NULL
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240 .. .. ..$ : NULL
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241 .. .. ..$ : NULL
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242 .. .. ..$ : NULL
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243 .. .. ..$ : NULL
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244 .. .. ..$ : NULL
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245 .. .. ..$ : NULL
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246 .. .. ..$ : NULL
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247 .. .. ..$ : NULL
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248 .. .. ..$ : NULL
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249 .. .. ..$ : NULL
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250 .. .. ..$ : NULL
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251 .. .. ..$ : NULL
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252 .. .. ..$ : NULL
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253 .. .. ..$ : NULL
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254 .. .. ..$ : NULL
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255 .. .. ..$ : NULL
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256 .. .. ..$ : NULL
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257 .. .. ..$ : NULL
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258 .. .. ..$ : NULL
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259 .. .. ..$ : NULL
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260 .. .. ..$ : NULL
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261 .. .. ..$ :List of 4
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262 .. .. .. ..$ y : num 2
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263 .. .. .. ..$ iso : num 0
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264 .. .. .. ..$ charge: Named num 1
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265 .. .. .. .. ..- attr(*, "names")= chr "charge"
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266 .. .. .. ..$ val : Named num 0
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267 .. .. .. .. ..- attr(*, "names")= chr "intrinsic"
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268 .. .. ..$ : NULL
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269 .. .. ..$ :List of 4
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270 .. .. .. ..$ y : num 2
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271 .. .. .. ..$ iso : Named num 1
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272 .. .. .. .. ..- attr(*, "names")= chr "iso"
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273 .. .. .. ..$ charge: Named num 1
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274 .. .. .. .. ..- attr(*, "names")= chr "charge"
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275 .. .. .. ..$ val : Named num 0
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276 .. .. .. .. ..- attr(*, "names")= chr "intrinsic"
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277 .. .. ..$ : NULL
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278 .. .. ..$ : NULL
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279 .. .. ..$ : NULL
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280 .. .. ..$ : NULL
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281 .. .. ..$ : NULL
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282 .. .. ..$ : NULL
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283 .. .. ..$ : NULL
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284 .. .. .. [list output truncated]
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285 .. ..@ derivativeIons : list()
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286 .. ..@ formula : list()
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287 .. ..@ sample : num NA
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288 .. ..@ xcmsSet :Formal class 'xcmsSet' [package "xcms"] with 12 slots
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289 .. .. .. ..@ peaks : num [1:9826, 1:13] 30.2 30.5 31.4 32.4 33.3 ...
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290 .. .. .. .. ..- attr(*, "dimnames")=List of 2
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291 .. .. .. .. .. ..$ : NULL
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292 .. .. .. .. .. ..$ : chr [1:13] "mz", "mzmin", "mzmax", "rt", "rtmin", "rtmax", "into", "intf", "maxo", "maxf", "i", "sn", "sample" (found with dput)
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293 From http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf:
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294
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295 mz weighted (by intensity) mean of peak m/z across scans
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296 mzmin m/z of minimum step
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297 mzmax m/z of maximum step
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298 rt retention time of peak midpoint
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299 rtmin leading edge of peak retention time
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300 rtmax trailing edge of peak retention time
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301 into integrated area of original (raw) peak
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302 intf integrated area of filtered peak
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303 maxo maximum intensity of original (raw) peak
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304 maxf maximum intensity of filtered peak
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305 i rank of peak identified in merged EIC (<= max)
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306 sn signal to noise ratio of the peak
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307
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308 .. .. .. ..@ groups : num [1:1828, 1:9] 30.2 30.5 31.4 32.4 33.4 ...
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309 .. .. .. .. ..- attr(*, "dimnames")=List of 2
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|
310 .. .. .. .. .. ..$ : NULL
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311 .. .. .. .. .. ..$ : chr [1:9] "mzmed" "mzmin" "mzmax" "rtmed" ...
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312 .. .. .. ..@ groupidx :List of 1828
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|
313 .. .. .. .. ..$ : int [1:4] 1 674 9671 9749
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|
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314 .. .. .. .. ..$ : int [1:4] 2 675 9672 9750
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315 .. .. .. .. ..$ : int [1:4] 3 676 9673 9751
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316 .. .. .. .. ..$ : int [1:4] 4 677 9674 9752
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317 .. .. .. .. ..$ : int [1:4] 6 678 9675 9753
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318 .. .. .. .. ..$ : int [1:4] 9 683 9676 9754
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319 .. .. .. .. ..$ : int [1:4] 11 684 9677 9755
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320 .. .. .. .. ..$ : int [1:4] 13 686 9678 9756
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321 .. .. .. .. ..$ : int [1:4] 17 688 9679 9757
|
|
|
322 .. .. .. .. ..$ : int [1:4] 18 689 9680 9758
|
|
|
323 .. .. .. .. ..$ : int [1:4] 19 691 9681 9759
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|
|
324 .. .. .. .. ..$ : int [1:4] 21 693 9682 9760
|
|
|
325 .. .. .. .. ..$ : int [1:4] 23 695 9683 9761
|
|
|
326 .. .. .. .. ..$ : int [1:4] 24 699 9684 9762
|
|
|
327 .. .. .. .. ..$ : int [1:4] 26 700 9685 9763
|
|
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328 .. .. .. .. ..$ : int [1:4] 28 702 9686 9764
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329 .. .. .. .. ..$ : int [1:4] 1353 3930 6183 7926
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330 .. .. .. .. ..$ : int [1:4] 36 707 9687 9765
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331 .. .. .. .. ..$ : int [1:4] 1354 3931 6184 7927
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332 .. .. .. .. ..$ : int [1:4] 1355 3932 6185 7928
|
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333 .. .. .. .. ..$ : int [1:4] 39 712 9688 9766
|
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334 .. .. .. .. ..$ : int [1:4] 1356 3934 6186 7929
|
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335 .. .. .. .. ..$ : int [1:4] 40 714 9689 9767
|
|
|
336 .. .. .. .. ..$ : int [1:4] 1358 3935 6187 7930
|
|
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337 .. .. .. .. ..$ : int [1:4] 1359 3936 6188 7931
|
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338 .. .. .. .. ..$ : int [1:4] 1361 3938 6189 7932
|
|
|
339 .. .. .. .. ..$ : int [1:4] 1360 3937 6190 7933
|
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|
340 .. .. .. .. ..$ : int [1:4] 45 722 9690 9768
|
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|
341 .. .. .. .. ..$ : int [1:4] 54 735 9691 9769
|
|
|
342 .. .. .. .. ..$ : int [1:4] 57 737 9692 9770
|
|
|
343 .. .. .. .. ..$ : int [1:4] 1365 3939 6191 7934
|
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|
344 .. .. .. .. ..$ : int [1:4] 1364 3940 6192 7935
|
|
|
345 .. .. .. .. ..$ : int [1:4] 1369 3941 6193 7936
|
|
|
346 .. .. .. .. ..$ : int [1:4] 58 739 9693 9771
|
|
|
347 .. .. .. .. ..$ : int [1:4] 1370 3942 6194 7937
|
|
|
348 .. .. .. .. ..$ : int [1:4] 1371 3943 6195 7938
|
|
|
349 .. .. .. .. ..$ : int [1:4] 1374 3944 6196 7939
|
|
|
350 .. .. .. .. ..$ : int [1:4] 65 748 9694 9772
|
|
|
351 .. .. .. .. ..$ : int [1:4] 1375 3946 6197 7940
|
|
|
352 .. .. .. .. ..$ : int [1:4] 71 755 9695 9773
|
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|
353 .. .. .. .. ..$ : int [1:5] 72 756 1376 1377 3947
|
|
|
354 .. .. .. .. ..$ : int [1:4] 1378 3948 6198 7941
|
|
|
355 .. .. .. .. ..$ : int [1:4] 1379 3950 6199 7942
|
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|
356 .. .. .. .. ..$ : int [1:4] 74 758 9696 9774
|
|
|
357 .. .. .. .. ..$ : int [1:4] 1381 3951 6200 7943
|
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|
358 .. .. .. .. ..$ : int [1:4] 1382 3952 6201 7944
|
|
|
359 .. .. .. .. ..$ : int [1:4] 78 761 9697 9775
|
|
|
360 .. .. .. .. ..$ : int [1:4] 1383 3955 6202 7945
|
|
|
361 .. .. .. .. ..$ : int [1:4] 1384 3956 6203 7946
|
|
|
362 .. .. .. .. ..$ : int [1:4] 1385 3957 6204 7947
|
|
|
363 .. .. .. .. ..$ : int [1:4] 1387 3958 6205 7948
|
|
|
364 .. .. .. .. ..$ : int [1:4] 1388 3959 6206 7949
|
|
|
365 .. .. .. .. ..$ : int [1:4] 1389 3960 6207 7950
|
|
|
366 .. .. .. .. ..$ : int [1:4] 1390 3962 6208 7951
|
|
|
367 .. .. .. .. ..$ : int [1:4] 1391 3963 6209 7952
|
|
|
368 .. .. .. .. ..$ : int [1:4] 1392 3965 6210 7953
|
|
|
369 .. .. .. .. ..$ : int [1:4] 90 776 9698 9776
|
|
|
370 .. .. .. .. ..$ : int [1:4] 1393 3966 6211 7954
|
|
|
371 .. .. .. .. ..$ : int [1:4] 1394 3967 6212 7955
|
|
|
372 .. .. .. .. ..$ : int [1:4] 1395 3968 6213 7956
|
|
|
373 .. .. .. .. ..$ : int [1:4] 1397 3970 6214 7957
|
|
|
374 .. .. .. .. ..$ : int [1:4] 1399 3972 6215 7958
|
|
|
375 .. .. .. .. ..$ : int [1:4] 1398 3971 6216 7959
|
|
|
376 .. .. .. .. ..$ : int [1:4] 101 788 9699 9777
|
|
|
377 .. .. .. .. ..$ : int [1:4] 100 790 9700 9778
|
|
|
378 .. .. .. .. ..$ : int [1:4] 1401 3973 6217 7960
|
|
|
379 .. .. .. .. ..$ : int [1:4] 1403 3975 6218 7961
|
|
|
380 .. .. .. .. ..$ : int [1:4] 1402 3974 6219 7962
|
|
|
381 .. .. .. .. ..$ : int [1:4] 1404 3976 6220 7963
|
|
|
382 .. .. .. .. ..$ : int [1:4] 1405 3977 6221 7964
|
|
|
383 .. .. .. .. ..$ : int [1:4] 1406 3978 6222 7965
|
|
|
384 .. .. .. .. ..$ : int [1:4] 1407 3979 6223 7966
|
|
|
385 .. .. .. .. ..$ : int [1:4] 1408 3980 6224 7967
|
|
|
386 .. .. .. .. ..$ : int [1:4] 1409 3981 6225 7968
|
|
|
387 .. .. .. .. ..$ : int [1:4] 1412 3982 6226 7969
|
|
|
388 .. .. .. .. ..$ : int [1:4] 1413 3983 6227 7970
|
|
|
389 .. .. .. .. ..$ : int [1:4] 1414 3984 6228 7971
|
|
|
390 .. .. .. .. ..$ : int [1:4] 1415 3985 6229 7972
|
|
|
391 .. .. .. .. ..$ : int [1:4] 1417 3987 6230 7973
|
|
|
392 .. .. .. .. ..$ : int [1:4] 1416 3988 6231 7974
|
|
|
393 .. .. .. .. ..$ : int [1:4] 1419 3989 6232 7975
|
|
|
394 .. .. .. .. ..$ : int [1:4] 1421 3991 6233 7976
|
|
|
395 .. .. .. .. ..$ : int [1:4] 1420 3990 6234 7977
|
|
|
396 .. .. .. .. ..$ : int [1:4] 1422 3992 6235 7978
|
|
|
397 .. .. .. .. ..$ : int [1:4] 115 802 9701 9779
|
|
|
398 .. .. .. .. ..$ : int [1:4] 1423 3993 6236 7979
|
|
|
399 .. .. .. .. ..$ : int [1:4] 1425 3995 6237 7980
|
|
|
400 .. .. .. .. ..$ : int [1:4] 1426 3996 6238 7981
|
|
|
401 .. .. .. .. ..$ : int [1:4] 120 807 9702 9780
|
|
|
402 .. .. .. .. ..$ : int [1:4] 1427 3997 6239 7982
|
|
|
403 .. .. .. .. ..$ : int [1:4] 1430 3998 6240 7983
|
|
|
404 .. .. .. .. ..$ : int [1:4] 1431 3999 6241 7984
|
|
|
405 .. .. .. .. ..$ : int [1:4] 123 812 9703 9781
|
|
|
406 .. .. .. .. ..$ : int [1:4] 1432 4000 6242 7985
|
|
|
407 .. .. .. .. ..$ : int [1:4] 1433 4001 6243 7986
|
|
|
408 .. .. .. .. ..$ : int [1:4] 1434 4002 6244 7987
|
|
|
409 .. .. .. .. ..$ : int [1:4] 1436 4005 6245 7988
|
|
|
410 .. .. .. .. ..$ : int [1:4] 1435 4004 6246 7989
|
|
|
411 .. .. .. .. ..$ : int [1:4] 1437 4006 6247 7990
|
|
|
412 .. .. .. .. .. [list output truncated]
|
|
|
413 .. .. .. ..@ filled : int [1:3644] 6183 6184 6185 6186 6187 6188 6189 6190 6191 6192 ...
|
|
|
414 .. .. .. ..@ phenoData :'data.frame': 4 obs. of 1 variable:
|
|
|
415 .. .. .. .. ..$ class: Factor w/ 2 levels "CLASS1","CLASS2": 1 1 2 2
|
|
|
416 .. .. .. ..@ rt :List of 2
|
|
|
417 .. .. .. .. ..$ raw :List of 4
|
|
|
418 .. .. .. .. .. ..$ : num [1:10136] 194 194 194 194 195 ...
|
|
|
419 .. .. .. .. .. ..$ : num [1:10138] 194 194 194 194 195 ...
|
|
|
420 .. .. .. .. .. ..$ : num [1:2614] 3.46 4.75 6.04 7.32 8.61 ...
|
|
|
421 .. .. .. .. .. ..$ : num [1:2613] 3.47 4.77 6.06 7.37 8.66 ...
|
|
|
422 .. .. .. .. ..$ corrected:List of 4
|
|
|
423 .. .. .. .. .. ..$ : num [1:10136] 168 169 169 169 169 ...
|
|
|
424 .. .. .. .. .. ..$ : num [1:10138] 157 158 158 158 158 ...
|
|
|
425 .. .. .. .. .. ..$ : num [1:2614] 40.5 41.8 43.1 44.4 45.7 ...
|
|
|
426 .. .. .. .. .. ..$ : num [1:2613] 40.7 42 43.3 44.6 45.9 ...
|
|
|
427 .. .. .. ..@ filepaths : chr [1:4] "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/zipOut/CLASS1/STDmix_GC_01.CDF" "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/zipOut/CLASS1/STDmix_GC_02.CDF" "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/zipOut/CLASS2/STDmix_RP_pos01.CDF" "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/zipOut/CLASS2/STDmix_RP_pos02.CDF"
|
|
|
428 .. .. .. ..@ profinfo :List of 2
|
|
|
429 .. .. .. .. ..$ method: chr "bin"
|
|
|
430 .. .. .. .. ..$ step : num 0.05
|
|
|
431 .. .. .. ..@ dataCorrection : int(0)
|
|
|
432 .. .. .. ..@ polarity : chr(0)
|
|
|
433 .. .. .. ..@ progressInfo :List of 12
|
|
|
434 .. .. .. .. ..$ group.density : num 0
|
|
|
435 .. .. .. .. ..$ group.mzClust : num 0
|
|
|
436 .. .. .. .. ..$ group.nearest : num 0
|
|
|
437 .. .. .. .. ..$ findPeaks.centWave : num 0
|
|
|
438 .. .. .. .. ..$ findPeaks.massifquant : num 0
|
|
|
439 .. .. .. .. ..$ findPeaks.matchedFilter: num 0
|
|
|
440 .. .. .. .. ..$ findPeaks.MS1 : num 0
|
|
|
441 .. .. .. .. ..$ findPeaks.MSW : num 0
|
|
|
442 .. .. .. .. ..$ retcor.obiwarp : num 0
|
|
|
443 .. .. .. .. ..$ retcor.peakgroups : num 0
|
|
|
444 .. .. .. .. ..$ fillPeaks.chrom : num 0
|
|
|
445 .. .. .. .. ..$ fillPeaks.MSW : num 0
|
|
|
446 .. .. .. ..@ progressCallback:function (progress)
|
|
|
447 .. ..@ ruleset : NULL
|
|
|
448 .. ..@ annoID : logi[0 , 1:4]
|
|
|
449 .. .. ..- attr(*, "dimnames")=List of 2
|
|
|
450 .. .. .. ..$ : NULL
|
|
|
451 .. .. .. ..$ : chr [1:4] "id" "grpID" "ruleID" "parentID"
|
|
|
452 .. ..@ annoGrp : logi[0 , 1:4]
|
|
|
453 .. .. ..- attr(*, "dimnames")=List of 2
|
|
|
454 .. .. .. ..$ : NULL
|
|
|
455 .. .. .. ..$ : chr [1:4] "id" "mass" "ips" "psgrp"
|
|
|
456 .. ..@ isoID : num [1:315, 1:4] 14 90 107 121 134 137 148 152 157 170 ...
|
|
|
457 .. .. ..- attr(*, "dimnames")=List of 2
|
|
|
458 .. .. .. ..$ : NULL
|
|
|
459 .. .. .. ..$ : chr [1:4] "mpeak" "isopeak" "iso" "charge"
|
|
|
460 .. ..@ polarity : chr ""
|
|
|
461 .. ..@ runParallel :List of 1
|
|
|
462 .. .. ..$ enable: num 0
|
|
|
463 .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
|
|
|
464 .. .. .. ..@ .Data:List of 1
|
|
|
465 .. .. .. .. ..$ : int [1:3] 1 13 333
|
|
|
466 $ Annotation:List of 5
|
|
|
467 ..$ annotation.table :'data.frame': 27 obs. of 13 variables:
|
|
|
468 .. ..$ feature : int [1:27] 190 193 195 206 208 209 212 367 368 371 ...
|
|
|
469 .. ..$ db_position : int [1:27] 21 22 23 21 23 24 22 1 2 4 ...
|
|
|
470 .. ..$ ChemSpiderID: int [1:27] 10463792 10463792 10463792 10463792 10463792 10463792 10463792 8711 8711 8711 ...
|
|
|
471 .. ..$ mz : num [1:27] 137 348 696 137 696 ...
|
|
|
472 .. ..$ rt : num [1:27] 10.8 10.8 10.8 11.2 11.2 ...
|
|
|
473 .. ..$ I : num [1:27] 10660 3754.5 32.4 5127 58.2 ...
|
|
|
474 .. ..$ compound : Factor w/ 4 levels "D-(+)-Catechin",..: 4 4 4 4 4 4 4 1 1 1 ...
|
|
|
475 .. ..$ db_mz : num [1:27] 137 348 696 137 696 ...
|
|
|
476 .. ..$ db_rt : num [1:27] 10.8 10.8 10.8 10.8 10.8 ...
|
|
|
477 .. ..$ db_I : num [1:27] 33.4 4478.7 58.2 33.4 58.2 ...
|
|
|
478 .. ..$ db_ann : Factor w/ 1 level "automatic": 1 1 1 1 1 1 1 1 1 1 ...
|
|
|
479 .. ..$ mz.err : num [1:27] 0.005 0.005 0.005 0.005 0.005 0.005 0.005 0.005 0.005 0.005 ...
|
|
|
480 .. ..$ clid : int [1:27] 1 1 1 2 2 2 2 2 2 2 ...
|
|
|
481 ..$ compounds : chr [1:4] "adenosine 2'-monophosphate" "D-(+)-Catechin" "malvidin-3-glucoside" "rutin "
|
|
|
482 ..$ ChemSpiderIDs : int [1:4] 10463792 8711 391785 4444362
|
|
|
483 ..$ multiple.annotations: num(0)
|
|
|
484 ..$ ann.features : int [1:27] 190 193 195 206 208 209 212 367 368 371 ...
|
|
|
485 $ Settings :Formal class 'metaMSsettings' [package "metaMS"] with 30 slots
|
|
|
486 .. ..@ protocolName : chr "Synapt.QTOF.RP"
|
|
|
487 .. ..@ chrom : chr "LC"
|
|
|
488 .. ..@ PeakPicking :List of 5
|
|
|
489 .. .. ..$ method : chr "matchedFilter"
|
|
|
490 .. .. ..$ step : num 0.05
|
|
|
491 .. .. ..$ fwhm : num 20
|
|
|
492 .. .. ..$ snthresh: num 4
|
|
|
493 .. .. ..$ max : num 50
|
|
|
494 .. ..@ Alignment :List of 9
|
|
|
495 .. .. ..$ min.class.fraction: num 0.3
|
|
|
496 .. .. ..$ min.class.size : num 3
|
|
|
497 .. .. ..$ mzwid : num 0.1
|
|
|
498 .. .. ..$ bws : num [1:2] 30 10
|
|
|
499 .. .. ..$ missingratio : num 0.2
|
|
|
500 .. .. ..$ extraratio : num 0.1
|
|
|
501 .. .. ..$ retcormethod : chr "linear"
|
|
|
502 .. .. ..$ retcorfamily : chr "symmetric"
|
|
|
503 .. .. ..$ fillPeaks : logi TRUE
|
|
|
504 .. ..@ CAMERA :List of 3
|
|
|
505 .. .. ..$ perfwhm : num 0.6
|
|
|
506 .. .. ..$ cor_eic_th: num 0.7
|
|
|
507 .. .. ..$ ppm : num 5
|
|
|
508 .. ..@ match2DB.rtdiff : num 1.5
|
|
|
509 .. ..@ match2DB.minfeat : num 2
|
|
|
510 .. ..@ match2DB.rtval : num 0.1
|
|
|
511 .. ..@ match2DB.mzdiff : num 0.005
|
|
|
512 .. ..@ match2DB.ppm : num 5
|
|
|
513 .. ..@ match2DB.simthresh : num(0)
|
|
|
514 .. ..@ match2DB.timeComparison : chr(0)
|
|
|
515 .. ..@ match2DB.RIdiff : num(0)
|
|
|
516 .. ..@ DBconstruction.minfeat : num(0)
|
|
|
517 .. ..@ DBconstruction.rttol : num(0)
|
|
|
518 .. ..@ DBconstruction.mztol : num(0)
|
|
|
519 .. ..@ DBconstruction.minintens : num(0)
|
|
|
520 .. ..@ DBconstruction.intensityMeasure : chr(0)
|
|
|
521 .. ..@ DBconstruction.DBthreshold : num(0)
|
|
|
522 .. ..@ matchIrrelevants.irrelevantClasses: chr(0)
|
|
|
523 .. ..@ matchIrrelevants.simthresh : num(0)
|
|
|
524 .. ..@ matchIrrelevants.timeComparison : chr(0)
|
|
|
525 .. ..@ matchIrrelevants.RIdiff : num(0)
|
|
|
526 .. ..@ matchIrrelevants.rtdiff : num(0)
|
|
|
527 .. ..@ betweenSamples.min.class.fraction : num(0)
|
|
|
528 .. ..@ betweenSamples.min.class.size : num(0)
|
|
|
529 .. ..@ betweenSamples.timeComparison : chr(0)
|
|
|
530 .. ..@ betweenSamples.rtdiff : num(0)
|
|
|
531 .. ..@ betweenSamples.RIdiff : num(0)
|
|
|
532 .. ..@ betweenSamples.simthresh : num(0)
|
