[BioC] Basic R question
Heidi Dvinge
heidi at ebi.ac.uk
Thu Jul 14 16:47:45 CEST 2011
If X is your data.frame, try
X.chrom <- split(X, X$chrom)
This will create a list, with a dataframe for eah unique entry in the
"chrom" column.
HTH
\Heidi
> HI ,
> I want to subset a list I have in order to look only the data from
> chosen chromosomes.
> my file is this format ( see attached for a workable example) . This
> dataframe contain 6 columns, ID (X10th.txt., X11th.txt..),
> chrom(1---X,Y), loc.start and loc.end( coordinate), num.mark and seg
> mean. I would like to create the same file ( with 6 columns) but only
> containing information from chromosome 1, then another one for 2 then
> 3...Y. Could somebody help please?
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=C
> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] cghMCR_1.8.0 limma_3.4.3 CNTools_1.6.0 genefilter_1.32.0
> [5] DNAcopy_1.24.0
>
> loaded via a namespace (and not attached):
> [1] annotate_1.26.0 AnnotationDbi_1.10.1 Biobase_2.8.0
> [4] DBI_0.2-5 RSQLite_0.9-1 splines_2.11.1
> [7] survival_2.35-8 xtable_1.5-6
>
> thanks a lot
> Nathalie
>
>
> ID chrom loc.start loc.end num.mark seg.mean
> 1 X10Th.txt 1 3002738 4.2E+07 3202 -0.0163
> 2 X10Th.txt 1 4.2E+07 4.2E+07 2 -0.7027
> 3 X10Th.txt 1 4.2E+07 1.7E+08 10731 0.0081
> 4 X10Th.txt 1 1.7E+08 1.7E+08 11 0.7461
> 5 X10Th.txt 1 1.7E+08 2.0E+08 2448 -0.0052
> 6 X10Th.txt 10 3002742 1.3E+08 11833 -0.0574
> 7 X10Th.txt 11 3026911 3100146 12 -0.4499
> 8 X10Th.txt 11 3102021 3.4E+07 2516 0.007
> 9 X10Th.txt 11 3.4E+07 3.4E+07 4 0.7885
> 10 X10Th.txt 11 3.4E+07 7.1E+07 3834 -0.0119
> 11 X10Th.txt 11 7.1E+07 7.1E+07 10 -1.5455
> 12 X10Th.txt 11 7.1E+07 8.3E+07 1618 0.0099
> 13 X10Th.txt 11 8.3E+07 8.4E+07 2 -1.9797
> 14 X10Th.txt 11 8.4E+07 9.0E+07 739 0.0197
> 15 X10Th.txt 11 9.0E+07 9.0E+07 3 0.4815
> 16 X10Th.txt 11 9.0E+07 1.2E+08 3920 -0.0171
> 17 X10Th.txt 12 3095298 6.3E+07 4424 0.0474
> 18 X10Th.txt 12 6.3E+07 6.3E+07 3 0.5165
> 19 X10Th.txt 12 6.3E+07 1.1E+08 5209 0.0385
> 20 X10Th.txt 12 1.1E+08 1.1E+08 6 -0.4526
> 21 X10Th.txt 12 1.1E+08 1.2E+08 201 0.1305
> 22 X10Th.txt 12 1.2E+08 1.2E+08 19 0.614
> 23 X10Th.txt 12 1.2E+08 1.2E+08 481 0.0334
> 24 X10Th.txt 13 3004789 1.2E+08 10642 -0.3045
> 25 X10Th.txt 14 3892581 5.2E+07 4281 0.5563
> 26 X10Th.txt 14 5.2E+07 5.2E+07 4 -0.4408
> 27 X10Th.txt 14 5.2E+07 5.2E+07 11 -1.4074
> 28 X10Th.txt 14 5.2E+07 5.3E+07 12 -0.6649
> 29 X10Th.txt 14 5.3E+07 5.3E+07 18 -1.5591
> 30 X10Th.txt 14 5.3E+07 5.3E+07 56 -2.6024
> 31 X10Th.txt 14 5.3E+07 6.8E+07 1815 0.5608
> 32 X10Th.txt 14 6.8E+07 6.8E+07 33 0.1478
> 33 X10Th.txt 14 6.8E+07 1.2E+08 4457 0.5724
> 34 X10Th.txt 15 3091692 3.9E+07 2821 0.6079
> 35 X10Th.txt 15 3.9E+07 3.9E+07 5 0.1051
> 36 X10Th.txt 15 3.9E+07 3.9E+07 12 0.5436
> 37 X10Th.txt 15 3.9E+07 3.9E+07 2 -0.8667
> 38 X10Th.txt 15 3.9E+07 1.0E+08 6464 0.6688
> 39 X10Th.txt 16 3151162 6024268 339 -0.1676
> 40 X10Th.txt 16 6032525 6045766 3 -2.3133
> 41 X10Th.txt 16 6056091 3.6E+07 3366 -0.136
> 42 X10Th.txt 16 3.6E+07 3.6E+07 4 -1.392
> 43 X10Th.txt 16 3.6E+07 9.8E+07 5329 -0.1383
> 44 X10Th.txt 17 3009074 9.5E+07 9007 -0.1542
> 45 X10Th.txt 18 3181133 9.1E+07 8058 -0.0622
> 46 X10Th.txt 19 3147156 1.7E+07 1848 -0.3487
> 47 X10Th.txt 19 1.7E+07 1.8E+07 100 -0.9124
> 48 X10Th.txt 19 1.8E+07 6.1E+07 4443 -0.3708
> 49 X10Th.txt 2 3010301 3.1E+07 2777 0.1381
> 50 X10Th.txt 2 3.1E+07 3.1E+07 4 -0.3156
> 51 X10Th.txt 2 3.1E+07 7.2E+07 3546 0.1484
> 52 X10Th.txt 2 7.2E+07 7.2E+07 2 -0.4492
> 53 X10Th.txt 2 7.2E+07 9.0E+07 1994 0.1389
> 54 X10Th.txt 2 9.0E+07 9.0E+07 2 0.7181
> 55 X10Th.txt 2 9.0E+07 9.1E+07 192 0.1815
> 56 X10Th.txt 2 9.1E+07 9.1E+07 4 0.6128
> 57 X10Th.txt 2 9.1E+07 1.8E+08 8335 0.1312
> 58 X10Th.txt 3 3007185 1.4E+08 11302 -0.1118
> 59 X10Th.txt 3 1.4E+08 1.4E+08 3 1.1729
> 60 X10Th.txt 3 1.4E+08 1.6E+08 1828 -0.1205
> 61 X10Th.txt 4 3012291 3335299 10 0.0708
> 62 X10Th.txt 4 3353037 9459467 498 0.6502
> 63 X10Th.txt 4 9469402 9469402 3 -0.1167
> 64 X10Th.txt 4 9473906 1.1E+07 123 0.8942
> 65 X10Th.txt 4 1.1E+07 1.4E+07 253 0.334
> 66 X10Th.txt 4 1.5E+07 1.6E+07 150 0.8265
> 67 X10Th.txt 4 1.6E+07 1.9E+07 179 0.322
> 68 X10Th.txt 4 1.9E+07 2.5E+07 463 0.8283
> 69 X10Th.txt 4 2.5E+07 2.5E+07 2 -4.1559
> 70 X10Th.txt 4 2.5E+07 3.7E+07 759 0.8149
> 71 X10Th.txt 4 3.7E+07 3.7E+07 20 1.2765
> 72 X10Th.txt 4 3.7E+07 5.9E+07 1833 0.4829
> 73 X10Th.txt 4 5.9E+07 6E+07 83 1.0287
> 74 X10Th.txt 4 6.0E+07 6.6E+07 455 0.623
> 75 X10Th.txt 4 6.6E+07 6.6E+07 3 -4.8121
> 76 X10Th.txt 4 6.6E+07 8.7E+07 1509 0.4519
> 77 X10Th.txt 4 8.7E+07 8.8E+07 37 0.9291
> 78 X10Th.txt 4 8.8E+07 9.7E+07 764 0.3171
> 79 X10Th.txt 4 9.7E+07 1.0E+08 417 0.8177
> 80 X10Th.txt 4 1.0E+08 1.0E+08 35 1.3066
> 81 X10Th.txt 4 1.0E+08 1.1E+08 1125 0.7607
> 82 X10Th.txt 4 1.1E+08 1.2E+08 933 0.3508
> 83 X10Th.txt 4 1.2E+08 1.2E+08 192 0.8091
> 84 X10Th.txt 4 1.2E+08 1.2E+08 15 1.3286
> 85 X10Th.txt 4 1.2E+08 1.2E+08 78 0.8328
> 86 X10Th.txt 4 1.2E+08 1.4E+08 1514 0.3228
> 87 X10Th.txt 4 1.4E+08 1.4E+08 3 1.2655
> 88 X10Th.txt 4 1.4E+08 1.5E+08 1352 0.283
> 89 X10Th.txt 4 1.5E+08 1.5E+08 41 0.8091
> 90 X10Th.txt 4 1.5E+08 1.6E+08 793 0.2844
> 91 X10Th.txt 5 3003879 3.3E+07 2707 0.105
> 92 X10Th.txt 5 3.3E+07 3.3E+07 3 -0.6753
> 93 X10Th.txt 5 3.3E+07 9.4E+07 5039 0.1072
> 94 X10Th.txt 5 9.4E+07 9.6E+07 8 -0.8031
> 95 X10Th.txt 5 9.6E+07 1.5E+08 6236 0.1028
> 96 X10Th.txt 6 3024849 2.6E+07 1843 -0.1733
> 97 X10Th.txt 6 2.6E+07 2.6E+07 2 -0.773
> 98 X10Th.txt 6 2.6E+07 3.4E+07 864 -0.1393
> 99 X10Th.txt 6 3.4E+07 3.4E+07 3 -2.5977
> 100 X10Th.txt 6 3.4E+07 4.1E+07 744 -0.1363
> 101 X10Th.txt 6 4.1E+07 4.1E+07 60 -0.9053
> 102 X10Th.txt 6 4.1E+07 1.2E+08 7693 -0.1561
> 103 X10Th.txt 6 1.2E+08 1.2E+08 2 0.5483
> 104 X10Th.txt 6 1.2E+08 1.5E+08 2924 -0.1333
> 105 X10Th.txt 7 3049177 2.9E+07 2215 -0.174
> 106 X10Th.txt 7 2.9E+07 2.9E+07 3 -0.8632
> 107 X10Th.txt 7 2.9E+07 3.4E+07 496 -0.1613
> 108 X10Th.txt 7 3.4E+07 3.5E+07 55 -0.6911
> 109 X10Th.txt 7 3.5E+07 1.0E+08 6236 -0.1745
> 110 X10Th.txt 7 1.0E+08 1.0E+08 5 -1.4229
> 111 X10Th.txt 7 1.0E+08 1.0E+08 20 -0.1964
> 112 X10Th.txt 7 1.0E+08 1.0E+08 6 -1.8286
> 113 X10Th.txt 7 1.0E+08 1.5E+08 4582 -0.1627
> 114 X10Th.txt 8 3111085 1.3E+08 11524 -0.1437
> 115 X10Th.txt 9 3088282 1.2E+08 12045 0.2501
> 116 X10Th.txt X 3086068 1.7E+08 12085 -0.0107
> 117 X10Th.txt Y 27 263780 52 -1.2383
> 118 X10Th.txt Y 263932 631098 15 -0.5181
> 119 X10Th.txt Y 631698 2177516 532 -1.256
> 120 X11Th.txt 1 3002738 2.0E+08 16394 -0.046
> 121 X11Th.txt 10 3002742 2.2E+07 1710 -0.2582
> 122 X11Th.txt 10 2.2E+07 2.2E+07 2 -2.3611
> 123 X11Th.txt 10 2.2E+07 1.3E+08 10121 -0.2586
> 124 X11Th.txt 11 3026911 3.4E+07 2528 -0.049
> 125 X11Th.txt 11 3.4E+07 3.4E+07 5 1.0058
> 126 X11Th.txt 11 3.4E+07 1.2E+08 10125 -0.035
> 127 X11Th.txt 12 3095298 6.3E+07 4424 -0.0904
> 128 X11Th.txt 12 6.3E+07 6.3E+07 3 1.7028
> 129 X11Th.txt 12 6.3E+07 1.2E+08 5916 -0.0654
> 130 X11Th.txt 13 3004789 1.3E+07 854 -0.1304
> 131 X11Th.txt 13 1.3E+07 1.3E+07 5 -1.3861
> 132 X11Th.txt 13 1.3E+07 2.8E+07 1591 -0.1782
> 133 X11Th.txt 13 2.8E+07 2.8E+07 5 -1.3185
> 134 X11Th.txt 13 2.8E+07 6.5E+07 3634 -0.1527
> 135 X11Th.txt 13 6.6E+07 6.7E+07 8 -1.1874
> 136 X11Th.txt 13 6.7E+07 6.9E+07 201 -0.1626
> 137 X11Th.txt 13 6.9E+07 6.9E+07 4 1.0844
> 138 X11Th.txt 13 6.9E+07 1.2E+08 4340 -0.1625
> 139 X11Th.txt 14 3892581 5.3E+07 4319 0.6606
> 140 X11Th.txt 14 5.3E+07 5.3E+07 58 -1.4906
> 141 X11Th.txt 14 5.3E+07 1.2E+08 6310 0.6554
> 142 X11Th.txt 15 3091692 8039326 448 0.4734
> 143 X11Th.txt 15 8040778 8040778 3 1.6185
> 144 X11Th.txt 15 8046698 3.9E+07 2358 0.454
> 145 X11Th.txt 15 3.9E+07 3.9E+07 3 1.5325
> 146 X11Th.txt 15 3.9E+07 1.0E+08 6492 0.4605
> 147 X11Th.txt 16 3151162 9.8E+07 9041 -0.2314
> 148 X11Th.txt 17 3009074 9.5E+07 9007 -0.0573
> 149 X11Th.txt 18 3181133 9.1E+07 8058 0.0341
> 150 X11Th.txt 19 3147156 6.1E+07 6391 -0.1194
> 151 X11Th.txt 2 3010301 5.0E+07 4560 0.1442
> 152 X11Th.txt 2 5.0E+07 5.0E+07 4 1.1306
> 153 X11Th.txt 2 5.0E+07 1.8E+08 12292 0.1487
> 154 X11Th.txt 3 3007185 6032558 245 -0.2823
> 155 X11Th.txt 3 6056822 6072724 3 1.2882
> 156 X11Th.txt 3 6083291 1.6E+08 12885 -0.2812
> 157 X11Th.txt 4 3012291 3146483 5 -0.8101
> 158 X11Th.txt 4 3159538 1.6E+08 13637 0.2846
> 159 X11Th.txt 5 3003879 1.1E+07 656 0.0416
>
>
>
>
>
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