motifAnnotations {RcisTarget} | R Documentation

## Annotations of Motifs to TFs

### Description

- motifAnnotations_hgnc: Annotations to HUMAN transcription factors for the rankings using motif collection version 9 ('mc9nr', 24453 motifs).

  Source: motifs-v9-nr.hgnc-m0.001-o0.0.tbl

- motifAnnotations_mgi: Contains the annotations to MOUSE transcription factors for the rankings using motif collection version 9 ('mc9nr', 24453 motifs).

  Source: motifs-v9-nr.mgi-m0.001-o0.0.tbl

- motifAnnotations_dmel: Contains the annotations to FLY transcription factors for the rankings using motif collection version 9 ('mc9nr', 24453 motifs).

  Source: motifs-v9-nr.flybase-m0.001-o0.0.tbl

- Previous versions: Annotations for motif collection version 8 ('mc8nr').

  - Human: motifAnnotations_hgnc_v8 (motifs-v8-nr.hgnc-m0.001-o0.0.tbl)

  - Mouse: motifAnnotations_mgi_v8 (motifs-v8-nr.mgi-m0.001-o0.0.tbl)

  - Fly: motifAnnotations_dmel_v8 (motifs-v8-nr.flybase-m0.001-o0.0.tbl)

These objects are meant to be provided to RcisTarget without modification, but it can also be explored by the user to obtain further information about the motifs. Columns:

- motif: Motif ID.

- TF: Transcription factor (or inferred gene).

- directAnnotation, inferred_Orthology, inferred_MotifSimil: Boolean values indicating whether the motif is annotated to the TF in the source database ("directAnnotation"), or whether it was inferred by orthology ("inferred_Orthology") or motif similarity ("inferred_MotifSimil").

- Description: Description of the source of the annotation.

- annotationSource: Source of the annotation formatted as factor (e.g. for subsetting). Levels: directAnnotation, inferredBy_Orthology, inferredBy_MotifSimilarity, inferredBy_MotifSimilarity_n_Orthology.

### Details

Documentation for the data

### See Also

importAnnotations, RcisTarget

[Package RcisTarget version 1.10.0 Index]