Best, Ramzi TEMANNI +31683862423 http://www.linkedin.com/in/ramzitemanni Hi Nathalie, sure you can easily do that by using the dir command: * files.list=dir(path = ".", pattern = "csv") * lest say you have files with extension csv the command dir will store the file names in myfiles then you loop over file.list and don't forget to change the paste part so you don't overwrite files. for (*myfile* in files.list) { data=read.table(...) .... for ... paste(*myfile*,"_",i,".**csv",sep="") ....} hope this answer your question. Best, Ramzi TEMANNI http://www.linkedin.com/in/**ramzitemanni On Thu, Jul 14, 2011 at 5:48 PM, Nathalie Conte wrote: > thanks Ramzi, the loop will save me a lot of time, is there a way to create > a loop to use read.table() of all tables in one go, for me to use them for > further analysis? > thanks again > Nat > >> 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 >> >> >> >> >> >> -- The Wellcome Trust Sanger Institute is operated by Genome >> Research >> Limited, a charity registered in England with number 1021457 and a >> company registered in England with number 2742969, whose >> registered office is 215 Euston Road, London, NW1 2BE. >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> > >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.**conductor >> >> >> > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research Limited, > a charity registered in England with number 1021457 and a company registered > in England with number 2742969, whose registered offic...{{dropped:7}}