importAnnotations: Imports the annotations of motifs to transcription factors

In RcisTarget: RcisTarget: Identify transcription factor binding motifs enriched on a gene list

Description

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

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-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)

RcisTarget documentation built on Nov. 8, 2020, 6:57 p.m.