Import Streme output from previous run
importStremeXML(streme_xml_path)path to streme.xml file
data.frame with statistics for each discovered motif. The `motifs` column contains a universalmotif object representation in PCM format of each DREME motif. If no motifs are discovered, returns NULL.
[runStreme()]
streme_xml <- system.file("extdata", "streme.xml", package = "memes")
importStremeXML(streme_xml)
#> motif name altname consensus
#> m1_RGCCACACCCWNNBY <mot:m1_R..> m1_RGCCACACCCWNNBY STREME-1 NRCCMCACCCWNHNN
#> m2_CTCCACCCAK <mot:m2_C..> m2_CTCCACCCAK STREME-2 CTCCACCCAK
#> m3_RGAGATAAGRVD <mot:m3_R..> m3_RGAGATAAGRVD STREME-3 RNAGATAAGRNN
#> m4_CCCKCCCTYC <mot:m4_C..> m4_CCCKCCCTYC STREME-4 CCCKCCCTYC
#> m5_AAAATRAAANMCA <mot:m5_A..> m5_AAAATRAAANMCA STREME-5 AAAATRAAAHNNA
#> m6_CCCCACCCC <mot:m6_C..> m6_CCCCACCCC STREME-6 CCCCACCCC
#> m7_AAAACAAACCTAG <mot:m7_A..> m7_AAAACAAACCTAG STREME-7 AAAACAAACCTAG
#> alphabet strand icscore nsites pval type pseudocount
#> m1_RGCCACACCCWNNBY DNA +- 14.728262 325 2.3e-09 PCM 0
#> m2_CTCCACCCAK DNA +- 16.726387 43 3.0e-02 PCM 0
#> m3_RGAGATAAGRVD DNA +- 12.702128 336 4.5e-02 PCM 0
#> m4_CCCKCCCTYC DNA +- 10.250530 378 4.7e-02 PCM 0
#> m5_AAAATRAAANMCA DNA +- 9.943566 361 2.2e-01 PCM 0
#> m6_CCCCACCCC DNA +- 11.494070 165 6.0e-01 PCM 0
#> m7_AAAACAAACCTAG DNA +- 17.153239 34 1.0e+00 PCM 0
#> bkg width initial_width
#> m1_RGCCACACCCWNNBY 0.256, 0.244, 0.244, 0.256 15 11
#> m2_CTCCACCCAK 0.256, 0.244, 0.244, 0.256 10 9
#> m3_RGAGATAAGRVD 0.256, 0.244, 0.244, 0.256 12 11
#> m4_CCCKCCCTYC 0.256, 0.244, 0.244, 0.256 10 7
#> m5_AAAATRAAANMCA 0.256, 0.244, 0.244, 0.256 13 9
#> m6_CCCCACCCC 0.256, 0.244, 0.244, 0.256 9 9
#> m7_AAAACAAACCTAG 0.256, 0.244, 0.244, 0.256 13 11
#> seed score_threshold pos_count neg_count
#> m1_RGCCACACCCWNNBY AGCCACACCCACTGC 11.5654 34 3
#> m2_CTCCACCCAK CTCCACCCAT 13.6193 5 0
#> m3_RGAGATAAGRVD GGAGATAAGAAT 8.98469 29 18
#> m4_CCCKCCCTYC CCCTCCCTCC 8.17623 30 19
#> m5_AAAATRAAANMCA AAAATGAAACGCA 8.38964 34 28
#> m6_CCCCACCCC CCCCACCCC 10.2743 9 9
#> m7_AAAACAAACCTAG AAAACAAACCTAG 13.2798 0 0
#> log_pval dtc bernoulli train_pos_count train_neg_count
#> m1_RGCCACACCCWNNBY -8.63457 -1 -1 291 31
#> m2_CTCCACCCAK -1.5299 -1 -1 38 1
#> m3_RGAGATAAGRVD -1.35111 -1 -1 307 130
#> m4_CCCKCCCTYC -1.33039 -1 -1 348 185
#> m5_AAAATRAAANMCA -0.664534 -1 -1 327 189
#> m6_CCCCACCCC -0.22349 -1 -1 156 66
#> m7_AAAACAAACCTAG 0 -1 -1 34 1
#> train_log_pval train_pval train_dtc train_bernoulli
#> m1_RGCCACACCCWNNBY -64.9779 1.1e-65 -1 -1
#> m2_CTCCACCCAK -10.3203 4.8e-11 -1 -1
#> m3_RGAGATAAGRVD -22.9027 1.3e-23 -1 -1
#> m4_CCCKCCCTYC -17.4235 3.8e-18 -1 -1
#> m5_AAAATRAAANMCA -12.9385 1.2e-13 -1 -1
#> m6_CCCCACCCC -10.4109 3.9e-11 -1 -1
#> m7_AAAACAAACCTAG -9.1239 7.5e-10 -1 -1
#> is_palindromic elapsed_time
#> m1_RGCCACACCCWNNBY no 3.9
#> m2_CTCCACCCAK no 16.8
#> m3_RGAGATAAGRVD no 9
#> m4_CCCKCCCTYC no 13.2
#> m5_AAAATRAAANMCA no 20.7
#> m6_CCCCACCCC no 23.8
#> m7_AAAACAAACCTAG no 27.2
#>
#> [Hidden empty columns: family, organism, bkgsites, qval, eval.]