R/data.R
example_ame_large.RdAME was run for "ectopic", "entopic", and "orphan" sites using shuffled background.
example_ame_largea list of runAme() results data.frames
see `vignette("integrative_analysis", package = "memes")` for details.
# Data can be combined into 1 large data.frame using:
dplyr::bind_rows(example_ame_large, .id = "binding_type")
#> # A tibble: 505 × 18
#> binding_type rank motif_db motif_id motif_alt_id consensus pvalue
#> <chr> <int> <chr> <chr> <chr> <chr> <dbl>
#> 1 ectopic 1 /nas/longleaf/h… Aef1_Fly… Aef1 CAACWACW 6.87e-23
#> 2 ectopic 2 /nas/longleaf/h… Aef1_SAN… Aef1 RCAACAAC… 1.69e-20
#> 3 ectopic 3 /nas/longleaf/h… CG7368_S… CG7368 KDGKGGGD… 2.71e-15
#> 4 ectopic 4 /nas/longleaf/h… klu_SOLE… klu KGYGKGGG… 1.35e-14
#> 5 ectopic 5 /nas/longleaf/h… l(3)neo3… l(3)neo38 DGKGGGKG… 2.1 e-14
#> 6 ectopic 6 /nas/longleaf/h… AbdB_SOL… Abd-B NTTWATKR 6.63e-14
#> 7 ectopic 7 /nas/longleaf/h… Mes2_SAN… Mes2 TTTARGCC… 2.34e-13
#> 8 ectopic 8 /nas/longleaf/h… Cad_Cell cad WTTWATTR 3.41e-13
#> 9 ectopic 9 /nas/longleaf/h… Cad_SOLE… cad DTTWATTR 4.67e-13
#> 10 ectopic 10 /nas/longleaf/h… klu_SANG… klu TGYGKGGG… 3.36e-12
#> # … with 495 more rows, and 11 more variables: adj.pvalue <dbl>, evalue <dbl>,
#> # tests <int>, fasta_max <dbl>, pos <int>, neg <int>, pwm_min <dbl>,
#> # tp <int>, tp_percent <dbl>, fp <int>, fp_percent <dbl>