Import tomtom data from previous run
importTomTomXML(tomtom_xml_path)path to tomtom.xml
will return data.frame with input motifs & results for best match. `tomtom` list column contains full tomtom data for each input motif. NOTE: if tomtom detects no matches for any input motif, currently will print a message & return NA values for `tomtom`, `best_match_name`, and `best_match_motif`.
tomtom list column format the `tomtom` list column contains data.frames with the following format: - name: name of query PWM - altname: alternate name of query PWM - match_name: name of matched PWM - match_altname: alt name of matched PWM - match_pval: p-value of match - match_eval: E-value of match - match_qval: q-value of match - match_offset: number of letters the query was offset from the target match - match_strand: whether the motif was found on input strand (+) or as reverse-complement (-) - db_name: database source of matched motif - match_motif: universalmotif object containing the PWM that was matched
[runTomTom()]
tomtom_xml <- system.file("extdata", "tomtom.xml", package = "memes")
importTomTomXML(tomtom_xml)
#> name altname family organism consensus alphabet strand icscore nsites
#> 1 AATAATAA DREME-2 <NA> <NA> AATAATAA DNA +- 16 10
#> 2 AAA DREME-1 <NA> <NA> AAA DNA +- 6 5
#> 3 AAT DREME-3 <NA> <NA> AAT DNA +- 6 10
#> bkgsites pval qval eval best_match_name best_match_altname
#> 1 NA NA NA 9 bab1_FlyReg FBgn0004870
#> 2 NA NA NA 39 <NA> <NA>
#> 3 NA NA NA 12 <NA> <NA>
#> best_match_motif
#> 1 <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>
#> 2 NULL
#> 3 NULL
#> best_db_name best_match_offset best_match_pval best_match_eval
#> 1 fly_factor_survey_id 0 0.000287 0.174
#> 2 <NA> NA NA NA
#> 3 <NA> NA NA NA
#> best_match_qval best_match_strand
#> 1 0.326 -
#> 2 NA <NA>
#> 3 NA <NA>
#> motif
#> 1 <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>
#> 2 <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>
#> 3 <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>
#> tomtom
#> 1 bab1_FlyReg, ap_FlyReg, Pph13_Cell, jigr1_SANGER_5, So_Cell, Antp_FlyReg, br-Z4_FlyReg, hb_FlyReg, zen_FlyReg, Hgtx_SOLEXA, eve_FlyReg, FBgn0004870, FBgn0000099_2, FBgn0023489, FBgn0039350, FBgn0003460, FBgn0000095_2, FBgn0000210_4, FBgn0001180_2, FBgn0004053_2, FBgn0040318_2, FBgn0000606_2, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, <S4 class ‘universalmotif’ [package “universalmotif”] with 20 slots>, fly_factor_survey_id, fly_factor_survey_id, fly_factor_survey_id, fly_factor_survey_id, fly_factor_survey_id, fly_factor_survey_id, fly_factor_survey_id, fly_factor_survey_id, fly_factor_survey_id, fly_factor_survey_id, fly_factor_survey_id, 0, -2, 0, 0, 0, -1, 0, -1, 0, 0, 1, 0.000287, 0.00413, 0.00419, 0.00431, 0.00657, 0.00825, 0.0086, 0.0102, 0.012, 0.0145, 0.0164, 0.174, 2.51, 2.55, 2.62, 4, 5.02, 5.23, 6.18, 7.31, 8.84, 9.99, 0.326, 0.592, 0.592, 0.592, 0.592, 0.592, 0.592, 0.592, 0.592, 0.592, 0.592, -, +, +, +, +, +, +, -, -, +, -
#> 2 NA, NA, NA, NA, NA, NA, NA, NA
#> 3 NA, NA, NA, NA, NA, NA, NA, NA