Transcription factor binding motif (TFBM) clustering


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Documentation for package ‘TFBMclust’ version 1.0

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TFBMclust-package Transcription factor binding motif (TFBM) clustering
align.leaf.and.cluster Align one single node with a cluster of (already aligned) motifs.
align.motifs Align all the motifs, using as base the merge order of one hierarchical tree.
align.two.clusters Align two already aligned clusters of motifs.
align.two.leaves Align two single nodes.
build.distance.matrix Build distance matrix from a motif comparison table
check.alignment Using a given agglomeration method, checks if the clusters will be aligned.
closest.or.farthest.motifs.ids Identify the "central" or farthest leaves (motifs) between two clusters.
color.code.clusters Assign one color to each cluster.
convert.hclust.to.JSON Convert 'hclust' tree to Newick format
convert.hclust.to.newick Convert 'hclust' tree to Newick format.
draw.heatmap.motifs Draw a heatmap of the input motifs, using the same distance tab and the same aggolmeration method.
fill.downstream Add gaps to the downstream end of the consensus
find.clusters Traverse the tree in a bottom-up approach to separate the motifs clusters.
get.comparison.number Given two sets of IDs, return the number of comparison from the given comparison table
get.comparison.numbers Given two sets of IDs, return the number of comparison from the given comparison table
get.consensus Extract the motif IUPAC consensus (or its reverse complement) from a reference table.
get.id Extract the id of a motif from a reference table.
get.name Extract the name of a motif from a reference table.
get.spacer.nb Counts the number of gaps ("-") in both ends of a consensus string.
hclust.motifs Hierarchical clustering of the motifs.
identify.JSON.tree.branches Identify the order of the branches in the JSON tree, relative to the order of one hclust tree.
inverted.alignment Invert the aligned consensus and orientation information for a group of aligned motifs.
leaves.per.node Collect the nodes of each node of the tree.
oct4.tfbm.compa Comparison matrix between 21 TFBM discovered by RSAT peak-motifs in Oct4 ChIP-seq peaks
TFBMclust Transcription factor binding motif (TFBM) clustering