# Transcription factor binding motif (TFBM) clustering

## Documentation for package ‘TFBMclust’ version 1.0

- DESCRIPTION file.

## Help Pages

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