importAnnotations: Imports the annotations of motifs to transcription factors

In aertslab/RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Imports the annotations of motifs to transcription factors

Description

RcisTarget package includes the motif annotations for the rankings using the latest motif collection (version 10 clustered, 19895 motifs):

• Human: data(motifAnnotations_hgnc)

• Mouse: data(motifAnnotations_mgi)

• Fly: data(motifAnnotations_dmel)

• Previous versions (Annotations for motif collection version 9 (24453 motifs) or 8: motifAnnotations_hgnc_v9 (Human), motifAnnotations_mgi_v9 (Mouse), motifAnnotations_dmel_v9 (Fly) 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: https://resources.aertslab.org/cistarget/motif2tf/

Usage

importAnnotations(annotFile, motifsInRanking = NULL, columnsToKeep = NULL)

Arguments

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. motifsInRanking=getRanking(motifRankings)$features
columnsToKeep	Other colums from the file to keep

Value

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 Also

See iRegulon paper and documentation for details on how the rankings and annotations were built.

Examples

# motifAnnotations <- importAnnotations("motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl")

## To save (decrease from ~100MB to 1MB): 
# save(motifAnnotations, file="motifAnnotations_hngc.RData", compress='xz')

# This code would generate the equivalent to
data(motifAnnotations_hgnc)

aertslab/RcisTarget documentation built on March 7, 2024, 11:21 p.m.