Get a data frame of all the motif datasets bundled with prego

The data frame contain the PSSMs ('A', 'C', 'G' and 'T' columns), with an additional column 'motif' containing the motif name. Individual datasets are available within the package as HOMER_motifs, JASPAR_motifs, JOLMA_motifs, and HOCOMOCO_motifs.

Usage

all_motif_datasets()

Value

a data frame which concatenates motifs from "HOMER", "JASPAR" and "JOLMA". Motif names are prefixed with the dataset name, e.g. "JASPAR.GATA4".

References

HOMER:: Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432
JASPAR:: Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung TY, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, and Mathelier A JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles Nucleic Acids Res. 2022 Jan 7;50(D1):D165-D173.; doi: 10.1093/nar/gkab1113
JOLMA:: Jolma, A., Yin, Y., Nitta, K. et al. DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature 534, S15–S16 (2016). doi:10.1038/nature18912
HOCOMOCO:: Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Ruslan N. Sharipov; Alla D. Fedorova; Eugene I. Rumynskiy; Yulia A. Medvedeva; Arturo Magana-Mora; Vladimir B. Bajic; Dmitry A. Papatsenko; Fedor A. Kolpakov; Vsevolod J. Makeev: HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucl. Acids Res., Database issue, gkx1106 (11 November 2017). doi:10.1093/nar/gkx1106

Examples

all_motif_datasets()
#> # A tibble: 49,269 × 8
#>    motif        pos     A     C     G     T dataset motif_orig
#>    <chr>      <dbl> <dbl> <dbl> <dbl> <dbl> <chr>   <chr>     
#>  1 HOMER.AP_1     0 0.419 0.275 0.277 0.028 HOMER   AP_1      
#>  2 HOMER.AP_1     1 0.001 0.001 0.001 0.997 HOMER   AP_1      
#>  3 HOMER.AP_1     2 0.01  0.002 0.965 0.023 HOMER   AP_1      
#>  4 HOMER.AP_1     3 0.984 0.003 0.001 0.012 HOMER   AP_1      
#>  5 HOMER.AP_1     4 0.062 0.579 0.305 0.054 HOMER   AP_1      
#>  6 HOMER.AP_1     5 0.026 0.001 0.001 0.972 HOMER   AP_1      
#>  7 HOMER.AP_1     6 0.043 0.943 0.001 0.012 HOMER   AP_1      
#>  8 HOMER.AP_1     7 0.98  0.005 0.001 0.014 HOMER   AP_1      
#>  9 HOMER.AP_1     8 0.05  0.172 0.307 0.471 HOMER   AP_1      
#> 10 HOMER.AP_1     9 0.149 0.444 0.211 0.195 HOMER   AP_1      
#> # ℹ 49,259 more rows