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


[Up] [Top]

Documentation for package ‘RcisTarget’ version 1.6.0

Help Pages

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
getAUC Class to store the AUC scores for RcisTarget.
getAUC-method Class to store the AUC scores for RcisTarget.
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.
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_hgnc Annotations of Motifs to TFs
motifAnnotations_hgnc_v8 Annotations of Motifs to TFs
motifAnnotations_mgi Annotations of Motifs to TFs
motifAnnotations_mgi_v8 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.
show-method Class to store the AUC scores for RcisTarget.
show-method Class to store the motif databases for RcisTarget.