importAnnotations: Imports the annotations of motifs to transcription factors

Description Usage Arguments Value See Also Examples

View source: R/00_importAnnotations.R

Description

RcisTarget package includes the motif annotations for the rankings using motif collection version 9 ('mc9nr', 24453 motifs):

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'):

Usage

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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:

See Also

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

Examples

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# 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)

aertslab/RcisTarget documentation built on April 21, 2021, 9:46 a.m.