[BioC] Basic R question
Nathalie Conte
nac at sanger.ac.uk
Thu Jul 14 16:34:09 CEST 2011
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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