Import Dreme output from previous run
importDremeXML(dreme_xml_path)path to dreme.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.
[runDreme()]
dreme_xml <- system.file("extdata", "dreme.xml", package = "memes")
importDremeXML(dreme_xml)
#> motif name altname consensus alphabet strand
#> m01_DGCARC <mot:m01_..> m01_DGCARC DREME-1 DGCARC DNA +-
#> m02_CACACRCA <mot:m02_..> m02_CACACRCA DREME-2 CACACACA DNA +-
#> m03_TTKTTGB <mot:m03_..> m03_TTKTTGB DREME-3 TTKTTGK DNA +-
#> m04_AGWGMGAG <mot:m04_..> m04_AGWGMGAG DREME-4 AGAGMGAG DNA +-
#> m05_GCVAAM <mot:m05_..> m05_GCVAAM DREME-5 GCVAAM DNA +-
#> m06_AAAHRAAA <mot:m06_..> m06_AAAHRAAA DREME-6 AAAWRAAA DNA +-
#> m07_CASACA <mot:m07_..> m07_CASACA DREME-7 CASACA DNA +-
#> m08_AAADTKG <mot:m08_..> m08_AAADTKG DREME-8 AAADTKG DNA +-
#> m09_CTCTCTB <mot:m09_..> m09_CTCTCTB DREME-9 CTCTCTB DNA +-
#> m10_MAAAAY <mot:m10_..> m10_MAAAAY DREME-10 MAAAAY DNA +-
#> icscore nsites bkgsites pval eval type pseudocount
#> m01_DGCARC 9.446498 1977 1351 6.7e-71 3.0e-66 PCM 0
#> m02_CACACRCA 15.476896 314 1351 6.8e-47 3.0e-42 PCM 0
#> m03_TTKTTGB 11.581994 946 1351 8.0e-51 3.6e-46 PCM 0
#> m04_AGWGMGAG 14.472835 349 1351 1.3e-40 5.6e-36 PCM 0
#> m05_GCVAAM 9.439360 1262 1351 3.6e-36 1.6e-31 PCM 0
#> m06_AAAHRAAA 13.508868 406 1351 1.0e-28 4.5e-24 PCM 0
#> m07_CASACA 11.023790 508 1351 4.5e-17 1.9e-12 PCM 0
#> m08_AAADTKG 11.438032 415 1351 1.4e-16 6.1e-12 PCM 0
#> m09_CTCTCTB 12.436647 265 1351 2.4e-15 9.9e-11 PCM 0
#> m10_MAAAAY 10.034118 970 1351 4.9e-15 2.1e-10 PCM 0
#> bkg rank seq length positive_hits
#> m01_DGCARC 0.267, 0.232, 0.234, 0.267 1 DGCARC 6 922
#> m02_CACACRCA 0.267, 0.232, 0.234, 0.267 2 CACACRCA 8 215
#> m03_TTKTTGB 0.267, 0.232, 0.234, 0.267 3 TTKTTGB 7 615
#> m04_AGWGMGAG 0.267, 0.232, 0.234, 0.267 4 AGWGMGAG 8 209
#> m05_GCVAAM 0.267, 0.232, 0.234, 0.267 5 GCVAAM 6 806
#> m06_AAAHRAAA 0.267, 0.232, 0.234, 0.267 6 AAAHRAAA 8 329
#> m07_CASACA 0.267, 0.232, 0.234, 0.267 7 CASACA 6 397
#> m08_AAADTKG 0.267, 0.232, 0.234, 0.267 8 AAADTKG 7 308
#> m09_CTCTCTB 0.267, 0.232, 0.234, 0.267 9 CTCTCTB 7 213
#> m10_MAAAAY 0.267, 0.232, 0.234, 0.267 10 MAAAAY 6 628
#> negative_hits unerased_evalue positive_total negative_total
#> m01_DGCARC 464 3e-66 1351 1351
#> m02_CACACRCA 19 9.9e-36 1351 1351
#> m03_TTKTTGB 255 9.7e-62 1351 1351
#> m04_AGWGMGAG 25 1.5e-36 1351 1351
#> m05_GCVAAM 482 3.4e-45 1351 1351
#> m06_AAAHRAAA 118 1.4e-41 1351 1351
#> m07_CASACA 216 2e-27 1351 1351
#> m08_AAADTKG 149 9.5e-19 1351 1351
#> m09_CTCTCTB 86 2.3e-24 1351 1351
#> m10_MAAAAY 431 2.4e-26 1351 1351
#> pos_frac neg_frac
#> m01_DGCARC 0.682457438934123 0.343449296817172
#> m02_CACACRCA 0.159141376757957 0.0140636565507032
#> m03_TTKTTGB 0.455218356772761 0.188749074759437
#> m04_AGWGMGAG 0.154700222057735 0.0185048112509252
#> m05_GCVAAM 0.59659511472983 0.356772760917839
#> m06_AAAHRAAA 0.243523316062176 0.0873427091043671
#> m07_CASACA 0.293856402664693 0.159881569207994
#> m08_AAADTKG 0.227979274611399 0.110288675055514
#> m09_CTCTCTB 0.157660991857883 0.0636565507031828
#> m10_MAAAAY 0.464840858623242 0.319022945965951
#>
#> [Hidden empty columns: family, organism, qval.]