motifclstest: Find motifs enriched in clustering
In spo111/DynaMO: DynaMO predicts spatiotemporal binding of transcription factors

Description Usage Arguments Details Value Author(s) Examples

Calculate enrichment levels of motifs in clusters generated by K-means clustering based on read counts at predicted motif sites across different samples.

1	motifclstest(motifcls, motifname)

`motifcls`	A matrix object with each row representing a motif site and each column representing read counts from one sample. The last three columns are the ids of clusters, the ids of motifs and the ids of motif sites.
`motifname`	A vector of ids of motifs. For example, if x motifs are examined, motifname is 1:x

This function counts the numbers of motif sites in each cluster for each motif and calculates the fold enrichments and p values for each motif in each cluster and outputs in a matrix where each row represents a motif.

A table is written in the "motif_cluster_enrichment.txt".

Zheng Kuang

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motiffdrread=read.table(system.file("extdata","motif_filter_reads_cluster.txt",
package="DynaMO",mustWork=TRUE),header=TRUE,sep="\t")
motiffdrclstest=motifclstest(motiffdrread,1:5)