RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions


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Documentation for package ‘RcisTarget’ version 1.28.0

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addLogo Add motif logo to RcisTarget results table
addMotifAnnotation Add motif annotation
addSignificantGenes Add significant genes
addSignificantGenes-method Add significant genes
aucScores Class to store the AUC scores for RcisTarget.
aucScores-class Class to store the AUC scores for RcisTarget.
calcAUC Calculate AUC
calcAUC-method Calculate AUC
cisTarget cisTarget
colnames-method Class to store the motif databases for RcisTarget.
convertToTargetRegions convertToTargetRegions
dbRegionsLoc Genomic location for the database regions
dbRegionsLoc_hg19_v9 Genomic location for the database regions
dbRegionsLoc_mm9_v9 Genomic location for the database regions
getAUC Class to store the AUC scores for RcisTarget.
getAUC-method Class to store the AUC scores for RcisTarget.
getColumnNames Import the motif databases for RcisTarget.
getDbRegionsLoc Gets the region location for the given database IDs.
getMaxRank Class to store the motif databases for RcisTarget.
getMaxRank-method Class to store the motif databases for RcisTarget.
getMotifAnnotation Get motif annotation
getNumColsInDB Class to store the motif databases for RcisTarget.
getNumColsInDB-method Class to store the motif databases for RcisTarget.
getRanking Class to store the motif databases for RcisTarget.
getRanking-method Class to store the motif databases for RcisTarget.
getRowNames Import the motif databases for RcisTarget.
getSignificantGenes Add significant genes
getSignificantGenes-method Add significant genes
importAnnotations Imports the annotations of motifs to transcription factors
importRankings Import the motif databases for RcisTarget.
motifAnnotations Annotations of Motifs to TFs
motifAnnotations_dmel Annotations of Motifs to TFs
motifAnnotations_dmel_v8 Annotations of Motifs to TFs
motifAnnotations_dmel_v9 Annotations of Motifs to TFs
motifAnnotations_hgnc Annotations of Motifs to TFs
motifAnnotations_hgnc_v8 Annotations of Motifs to TFs
motifAnnotations_hgnc_v9 Annotations of Motifs to TFs
motifAnnotations_mgi Annotations of Motifs to TFs
motifAnnotations_mgi_v8 Annotations of Motifs to TFs
motifAnnotations_mgi_v9 Annotations of Motifs to TFs
ncol-method Class to store the motif databases for RcisTarget.
nrow-method Class to store the motif databases for RcisTarget.
rankingRcisTarget Class to store the motif databases for RcisTarget.
rankingRcisTarget-class Class to store the motif databases for RcisTarget.
reRank Re-rank RcisTarget ranking
rownames-method Class to store the motif databases for RcisTarget.
show-method Class to store the AUC scores for RcisTarget.
show-method Class to store the motif databases for RcisTarget.
showLogo Show RcisTarget as HTML