Hi Nathalie,
this code sould give you the expected results:
data=read.table("data.csv",header=T) # read data file

for (i in unique(data$chrom) )
{
write.table(data[which(data$chrom==i),],paste("data",i,".csv",sep=""),row.names=F)
# generate 1 file per Chr
}





Best,
Ramzi TEMANNI
http://www.linkedin.com/in/ramzitemanni



On Thu, Jul 14, 2011 at 4:34 PM, Nathalie Conte <nac@sanger.ac.uk> wrote:

> 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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> in England with number 2742969, whose registered office is 215 Euston Road,
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