I'm new to R and using the cosmo package to find repeated subsequences in sequences of letters http://www.bioconductor.org/packages/2.10/bioc/html/cosmo.html To run it with the dataset below I just execute 3 commands:
library(cosmo)
seqal <- system.file("Exfiles/short1.FASTA", package="cosmo")
res <- cosmo(seqs=seqal, constraints="None", minW=10, maxW=10, models="TCM")
As result I get a list of motifs that I paste below but I need ALL the motifs not only the first 16, as I understand from the documentation "motifs" is a Character object how could I display it completely?
-1 1146 91 1 TTTTATTTTT 0.9797432
-2 1145 89 1 TTTTTTTTTT 0.9762943
-3 1187 87 1 TTTTTTTTTA 0.8750529
-4 1145 26 1 TTTTTTTTTA 0.8741454
-5 1196 73 -1 CAAAAAAAAA 0.8727398
-6 1196 97 -1 CAAAAAAAAA 0.8628938
-7 1250 79 -1 TAAAAAAAAA 0.8587207
-8 1157 40 -1 TAAAATAAAA 0.7922084
-9 1256 92 -1 AAAACTAAAA 0.7366366
-10 1145 102 1 TTTTTTTTAA 0.6705112
-11 1250 13 -1 TAACCAAAAA 0.6118567
-12 1114 70 -1 AAACCAAAAA 0.5864355
-13 1088 86 -1 CAAACTAAAA 0.5631808
-14 1122 73 -1 AAACAAAAAA 0.5310371
-15 1088 124 1 TATTATTTTA 0.4966246
-16 1187 8 -1 CAACAAAAAA 0.4187826
1068 CACCACAACCACCACCACCCCCCACTTCATATATCAATATACAACCAACATCCTCCCTCAAACTAATCCAAAACCTCCCCCCAAAAA
1073 CCAAAAAACAAATCAAAAATCCAATAATTCCACTTTTTAAATTACCTTCTCTATATATAACTCAAACAACA
1088 CCCACAATCACCTCCTCCTTCTCCCTAATATACACCCCCACACCACACATCCAATCAATCATCTTTTTTTCCAAAATTTTTCCCCCAAACTAAAAACATATCCCCATACCCCCCCCCCCCCCTTATTATTTTAA
1114 ACTCACACAAAATTCCCAATCTAAAATCACATTCACTATTCACTTTCTAATATTTCCTTAAAATACATAAAACCAAAAATCCTATTTTCACTACACAC
1122 CAAAAACCCCAAAAACCTTTCCTTTCTTCCCCTTTAAAATAAACTCCATCAACCCTAAATAAAAATCCTCCCAAACAAAAAA
1145 TTTCCTCTTTTTTTTTTTTTTCTCCTTTTTTTTTATTATTTATTATATATCTTAACATTTAATAATTACTTAATTTTATATTCTCTCCTTTTTTTTTTCTCTTTTTTTTAAATTTCCTAATTTTAATTATTTCACAATTCTAATTTCCACATTTATA
1146 CCCTACTCATACTCTCCACTACCCAACACTCCTTCAATTAAATTTAATTCATTACCTTATACTACCATTAACACCCAAAAAATTTCTCACTTTTATTTTTAATTTTTCTATCAAATTAAATCCATCCATTA
1157 CTCTAATTTTCATCCATTTCCCACCTTTACAACAAAACCTAAAATAAAATTTCCCAATTCAACTTCCAAACAATCTCTTAATTATCTTCCAATAATACTCATTAAAAAAATTCTCCAACCAACC
1161 ACACTCATATCCAATTTATATCTCCAAAAAACTCATATAATACCCTACATTACTTATTCCCAACCACCTACAACAAAATCTCATCATTTAAA
1164 TCTCCTATCTTCTTATAA
1187 AAAACCACAACAAAAAAACCAAAAAACCCAAAAACTCCCCTTCTCCTTCTCTCAATAAATCATAATTCTCCTTTTCTCCTTTCTTCTTTTTTTTTATACCATAAATATACCTAATAA
1196 CTCCACACACTCTACAAATCATCAACTATCCCCCAACACTCTCCCTTCCCCTTCCCCCCCCTAAACTAATCCCAAAAAAAAACCCCACCACAACCCCAAAAAAAAA
1206 CTTCAAACCCCACAAACCTACATATACCTACAAAATTCACCAACAA
1250 CCAACTTCATCATAACCAAAAATCCATACCCACTTAACATCCACATTATATAACAACAACCCCCAATATATACCTAATTAAAAAAAAACCACTAACAAAA
1256 ACCAAAAACCCTTACAAAACTCCATAACACCTCAACAAACAAAAAAAAAAAAACCCACAAAACCCCTCAAAACACAAAAAACAATCACAAAAAAACTAAAAAAA
1258 CCCTATATAATTACTACTATACTAACCCTTTCATTTAACCCTCTAATCTCCAATCTTACTACCCTACTCACACCCTCTACCTACACCCTAACTAACTCCTAATCTAACACTCCCAAATCACTA
1293 TCTATCATCATATTCCTACATTATACTCACTCTCCTCCCTTCCCCTTCAACCTATTCAAATCTTCTCCCACCCCCTCCCCTCTTATTCCATTANG
Thanks Ana
