importAnnotations {RcisTarget} | R Documentation |
RcisTarget package includes the motif annotations for the rankings using motif collection version 9 ('mc9nr', 24453 motifs):
Human: data(motifAnnotations_hgnc)
Mouse: data(motifAnnotations_mgi)
Fly: data(motifAnnotations_dmel)
Previous versions (Annotations for motif collection version 8: motifAnnotations_hgnc_v8 (Human), motifAnnotations_mgi_v8 (Mouse), motifAnnotations_dmel_v8 (Fly)
This function (importAnnotations) allows to import annotations for other versions of the rankings, or to keep extra data columns.
e.g. Source of the annotations (motif collection 9 'mc9nr'):
Human: https://resources.aertslab.org/cistarget/motif2tf/motifs-v9-nr.hgnc-m0.001-o0.0.tbl
Mouse: https://resources.aertslab.org/cistarget/motif2tf/motifs-v9-nr.mgi-m0.001-o0.0.tbl
importAnnotations(annotFile, motifsInRanking = NULL, columnsToKeep = NULL)
annotFile |
File containing the motif annotations corresponding to the rankings. They should match in organism and version. |
motifsInRanking |
Subset of motifs to keep.
e.g.
|
columnsToKeep |
Other colums from the file to keep |
data.table with the annotations of the motifs to transcription factors
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.
See iRegulon paper and documentation for details on how the rankings and annotations were built.
# motifAnnotations <- importAnnotations("motifs-v9-nr.hgnc-m0.001-o0.0.tbl") ## To save (decrease from ~100MB to 1MB): # attr(motifAnnotations, "version") <- "motifs-v9-nr.hgnc-m0.001-o0.0.tbl" # save(motifAnnotations, file="hgnc_motifAnnotations.RData", compress='xz') # This code would generate the equivalent to data(motifAnnotations_hgnc)