This is a light wrapper around [universalmotif::read_meme()] that imports MEME results as universalmotif data.frame. If MEME is run with genomic coordinates in the fasta header, in "chr:start-end" format (base 1 indexed), the genomic coordinates of the motif match from input sequences can be parsed from the header.
importMeme(meme_txt, parse_genomic_coord = FALSE, combined_sites = FALSE)path to "meme.txt" output
whether to parse sequence headers into genomic coordinates for motif position information, only works if fasta files were written such that the sequence headers are in the form: "chr:start-end", or some variation of this form (delimiters can be any of: "[^[:alnum:]]+" (ie non-alphanumeric characters)), (default = FALSE).
whether to add `combined_sites` output which contains coordinates of each sequence, the motif sequence (if `parse_genomic_coord = TRUE`), and the `diagram` column raw output from MEME indicating the relative locations of motifs in the sequence.
MEME results in universalmotif data.frame format (see: [as_universalmotif_dataframe()]). `sites_hits` is a nested data.frame column containing the position within each input sequence of matches to the identified motif.
[runMeme()] [universalmotif::read_meme()]
example_meme_txt <- system.file("extdata", "meme_full.txt", package = "universalmotif")
importMeme(example_meme_txt)
#> motif name altname consensus alphabet strand icscore
#> 1 <mot:1> 1 MEME AAAAAAAAAARAAAS DNA +- 19.23570
#> 2 <mot:2> 2 MEME YNHTCNCNNYNTSACNCKTBYYYTYCNTY DNA +- 13.88457
#> 3 <mot:3> 3 MEME CAMMAMAAAAA DNA +- 14.81432
#> nsites eval type pseudocount bkg width
#> 1 50 5.3e-32 PPM 1 0.343, 0.157, 0.157, 0.343 15
#> 2 44 4.8e-07 PPM 1 0.343, 0.157, 0.157, 0.343 29
#> 3 48 7.6e+01 PPM 1 0.343, 0.157, 0.157, 0.343 11
#> sites_hits
#> 1 AT1G21910, AT5G57560, AT4G29780, AT4G29780, AT3G48650, AT2G25735, AT2G20670, AT2G20670, AT2G40000, AT1G80440, AT1G80440, AT1G27730, AT3G04640, AT1G56060, AT1G66090, AT1G25400, AT4G24570, AT1G24140, AT5G25240, AT1G56240, AT4G14450, AT4G08950, AT3G48650, AT1G80440, AT3G46090, AT5G56550, AT5G52050, AT3G48650, AT2G20670, AT2G20670, AT1G25400, AT3G04640, AT2G44840, AT5G25240, AT3G55980, AT5G61600, AT4G27654, AT3G55980, AT2G44840, AT1G66090, AT3G48650, AT2G40000, AT1G24140, AT1G66090, AT1G56240, AT3G55980, AT2G32200, AT2G40000, AT4G13395, AT4G08950, 744, 377, 510, 131, 951, 56, 455, 141, 853, 292, 911, 528, 766, 99, 197, 578, 762, 659, 30, 461, 572, 883, 166, 255, 363, 737, 640, 203, 356, 41, 630, 64, 313, 781, 52, 948, 48, 943, 873, 896, 5, 810, 622, 506, 123, 905, 343, 256, 889, 386, 5.51e-08, 1.35e-07, 1.35e-07, 1.35e-07, 1.35e-07, 1.35e-07, 1.35e-07, 1.35e-07, 1.35e-07, 1.35e-07, 2.35e-07, 2.45e-07, 3.77e-07, 7.55e-07, 8.88e-07, 8.88e-07, 1.22e-06, 1.22e-06, 1.39e-06, 1.39e-06, 1.58e-06, 1.75e-06, 1.75e-06, 1.75e-06, 1.99e-06, 2.13e-06, 2.13e-06, 2.13e-06, 2.36e-06, 2.36e-06, 2.9e-06, 3.15e-06, 3.15e-06, 3.62e-06, 3.92e-06, 4.35e-06, 4.35e-06, 4.35e-06, 4.35e-06, 4.35e-06, 4.64e-06, 4.64e-06, 5.39e-06, 5.87e-06, 5.87e-06, 6.72e-06, 7.08e-06, 7.65e-06, 8.74e-06, 1.15e-05, GAAAAAAAAAGAAAC, AAAAAAAAAAAAAAC, AAAAAAAAAAAAAAC, AAAAAAAAAAAAAAC, AAAAAAAAAAAAAAC, AAAAAAAAAAAAAAC, AAAAAAAAAAAAAAC, AAAAAAAAAAAAAAC, AAAAAAAAAAAAAAC, AAAAAAAAAAAAAAC, AAAAAAGAAAGAAAC, AAAAAAGAAAGAAAG, AAAAAAAAAAGAGAG, AAAAAAAAGAGCAAG, AAAAGAAAAAAAAAC, CAAGAAAAAAGAAAC, GAAAACAAAAGAAAC, AAAAAAAACAAAAAC, CAAAAAAAGAAAAAG, CAAAAAAAAAACAAG, CAAAACAAAAGAAAG, GAAAAAAAGAGAGAG, AAAAAAGAAAACAAC, AAAAAAAAGAACAAG, GAAAAAAACAGCAAC, CAAAAAAACAAAAAC, CAAGAAAAAAAAAAC, AAAAGAAGAAGAAAG, AAAAAAAAAAAAAAA, AAAAAAAAAAAAAAA, GAAAGAAGAAGAAAC, AAAAATAAAAGAAAG, AAAAAAGAGAGAGAG, AAAGAGAAAAGAAAG, CAAAAAAAAAAAAAA, AAAAAACAAAGAGAG, AAAAGAAACAAAAAG, AAAAAAAAGACCAAG, AAAAAAAGAAGAAAA, GAAAAAAGAACAAAC, CAAAAAAAAAGGAAG, AAAAACGAAAAAAAG, AAAAAGAAAAAAGAC, AAAAATAAAAAAAAG, AAAAGAAAAACCAAG, GAAGAACAAAGAAAG, AAAAGAAAAAGCAAA, GAAAAAGAGAGAAAA, GAAGAAGAAACAAAC, GAAAAGAGAAGAGAG
#> 2 AT4G29780, AT5G25240, AT4G25490, AT3G55980, AT2G40000, AT1G74930, AT4G24570, AT4G25490, AT1G76650, AT1G74930, AT1G35140, AT4G32480, AT4G13395, AT3G44260, AT1G25400, AT5G45630, AT4G25490, AT4G25490, AT2G32200, AT2G20670, AT3G55980, AT2G44130, AT1G74930, AT3G15500, AT5G45630, AT1G72910, AT1G80840, AT1G21910, AT4G14450, AT1G27730, AT1G56240, AT4G32480, AT4G25490, AT3G15500, AT1G27730, AT1G72910, AT5G56550, AT1G35140, AT5G57560, AT4G27270, AT5G25240, AT1G35210, AT1G32920, AT1G80840, 887, 805, 149, 128, 924, 517, 846, 827, 159, 937, 494, 815, 939, 884, 702, 280, 921, 71, 2, 880, 804, 936, 53, 409, 322, 273, 813, 925, 959, 920, 39, 899, 210, 488, 746, 806, 115, 579, 880, 178, 856, 935, 140, 916, 1.47e-12, 2.43e-09, 2.43e-09, 1.02e-08, 2.73e-08, 4.37e-08, 7.76e-08, 8.68e-08, 8.68e-08, 1.21e-07, 1.35e-07, 1.68e-07, 1.88e-07, 1.88e-07, 2.09e-07, 2.87e-07, 4.35e-07, 4.81e-07, 4.81e-07, 5.33e-07, 5.9e-07, 5.9e-07, 5.9e-07, 6.52e-07, 7.96e-07, 7.96e-07, 7.96e-07, 9.69e-07, 1.18e-06, 1.18e-06, 1.3e-06, 1.43e-06, 1.89e-06, 1.89e-06, 1.89e-06, 2.74e-06, 3.01e-06, 3.01e-06, 3.29e-06, 3.6e-06, 4.31e-06, 4.71e-06, 6.13e-06, 1.21e-05, CGTTCACACCTTCACGCGCTTCCTTCGTC, CGCTCCCGCCTTCACAGCTGTCTTTCATC, TCTTCACCTTACCACTCTTTTTTTCCCTC, CTCACACAACATGACTCTCCTCCTTGGTT, CACACGCCTTTTTTCTCGTCCCCATCCTC, TGATCAACAGACGACTCGCTTCTTTCTTC, CTGTCTCACTCACACACGCGTTTTCCTAC, CACTCGCTGTCTGACGTGTGTCCTTTGAC, CATTCACTTTCTCACCCTTGCTCTCTTCT, TCTTCCTCACTTGCCACTTCCACTTCTTC, TCTTCGCCACATAAATCTTGCACTTTCTC, CAATCATATACTGACACGTCATCTTCTTC, CGCGTCCGACATCACACGCTCTCTTCTAT, ACCCCACCACTTGACGCGTTTCTCGTCCC, TCGTCACCTCCTCAGTGATTCCTCCGATC, CATTCTCAACGTCACGCGTGTACGCGGTT, TGCTCCCCACATATCCGTTATCTCTCCTC, CCCACCAGCCTTCACTGGCCCCATACGTC, CCATCTTCACTTGTCTCTTTTCCATCATG, CAATCACAGTTTCACACGTCACCATTCGC, CGCTCTTGTGCTGACTCTTCTACTCGTAT, CAACCGCAAGCAAACTCATCCTCCTCTTT, CGACCACAACAACAAGAATCTTCTCCTTC, CTACCACAAGCCGACACATGTCTTGTGTC, GCGTTTCCTCCTGACGCGCCGCTCTGTTT, CATCCACATCCTCTCTCACTTTCTTTATG, TCAACTCGGCTTCTATCGGGTCCACCCGC, TCATCTCTTCCTCTCCCATACCCCTCCCA, TCAACATGTTACAAGTCGTGGCCCTCCTC, CCTACCACTTGTCACGCAACTTCCTTCTC, CAGTTCACTAATCACACTTTCTCTTGTTC, TCTCCCACCTCTCAGGCGGGTCCCTAACC, CTCTCTCGTTACCTCTCGCTCTCACGTTA, CCATCATTCACTTACACGTGTTTTTTCTT, CTTGCACACACACACACGTGTACTAGGTC, CTTTGGCGGCCCATCTATTCTCTTCCCTC, TCCTTAAACCAAGAATCTTGTCCCTCTTT, CGAACATTACATGACTTTCTTCTTCCCAC, TGTTGCCTCAAAGACGCGGCTTCTTCTTT, CAACCCAATTTCCACGATTTTCTTCCTAC, CGCTCCTCTCACATCACTGTCACACTCTT, CCATCCACGACCAAATCATTCTCTCCATT, TCGACCCTCCAACTCCATTGCCTATCTAC, GCTCCTCTCTCTCTCTTCTGCCTCTTTCC
#> 3 AT4G13395, AT3G46090, AT1G66090, AT1G80440, AT4G24570, AT1G24140, AT5G54490, AT4G24570, AT1G35140, AT1G56240, AT1G69490, AT2G32200, AT5G25240, AT5G35777, AT4G32480, AT4G14450, AT3G15500, AT3G46090, AT1G76650, AT1G27730, AT2G44840, AT1G80440, AT4G27654, AT2G25735, AT1G27730, AT5G45630, AT4G27270, AT4G29780, AT3G50050, AT4G25490, AT1G56240, AT1G80840, AT1G80840, AT3G50050, AT1G33760, AT5G57560, AT5G25240, AT3G15500, AT3G55980, AT2G44840, AT5G51190, AT4G27270, AT3G48650, AT3G04640, AT1G66090, AT5G45630, AT1G21910, AT4G14450, 693, 611, 58, 524, 351, 150, 986, 983, 987, 893, 286, 442, 301, 641, 183, 853, 756, 659, 899, 811, 719, 892, 34, 289, 244, 190, 422, 989, 145, 296, 710, 354, 187, 747, 385, 402, 544, 525, 765, 804, 986, 761, 550, 3, 794, 174, 499, 467, 2.36e-06, 2.36e-06, 2.36e-06, 2.36e-06, 3.44e-06, 3.44e-06, 4.52e-06, 4.52e-06, 4.52e-06, 6.1e-06, 6.1e-06, 7.67e-06, 1.33e-05, 1.33e-05, 1.33e-05, 1.33e-05, 1.33e-05, 1.33e-05, 1.33e-05, 1.38e-05, 1.64e-05, 1.64e-05, 1.93e-05, 1.93e-05, 2e-05, 2.34e-05, 2.34e-05, 2.34e-05, 2.34e-05, 2.6e-05, 2.6e-05, 2.6e-05, 2.6e-05, 2.71e-05, 2.71e-05, 3.08e-05, 3.08e-05, 3.08e-05, 3.08e-05, 3.08e-05, 3.18e-05, 3.94e-05, 3.94e-05, 4.25e-05, 4.25e-05, 5.18e-05, 5.18e-05, 7.17e-05, CACAAAAAAAA, CACAAAAAAAA, CACAAAAAAAA, CACAACAAAAA, CACCAAAAAAA, CACCAAAAAAA, CACAACACAAA, CACAAAACAAA, CACAACACAAA, CACCAAACAAA, CACAACCAAAA, CCCAAAAAAAA, CAAAAAAAAAA, CAAAACAAAAA, CAAAAAAAAAA, CAAAACAAAAA, CAAAAAAAAAA, CAAAAAAAAAA, CAAAAAAAAAA, CCCCAAAAAAA, CAACAAAAAAA, CAACACAAAAA, CAAAAAACAAA, CAAAAAACAAA, CCCAACCAAAA, CAAAACCAAAA, CAACACACAAA, CAAAACCAAAA, CAAAAACAAAA, GACAAAAAAAA, GACAAAAAAAA, GACAAAAAAAA, GACAAAAAAAA, CAACAACAAAA, CAACAACAAAA, GACCACAAAAA, GACCAAAAAAA, CCAAAAAAAAA, GACCAAAAAAA, CCAAACAAAAA, CAAAAACCAAA, CACACAAAAAA, CCAAAAACAAA, CACCCCAAAAA, CCAAAACAAAA, CACAACACAAC, CACAAAACAAC, CACGAACAAAA
#>
#> [Hidden empty columns: family, organism, bkgsites, pval, qval.]