drawVolcanoPlot {transite} | R Documentation

## k-mer Enrichment Volcano Plot

### Description

Uses a volcano plot to visualize k-mer enrichment. X-axis is \log_2 enrichment value, y-axis is \log_10 significance, i.e., multiple testing corrected p-value from Fisher's exact test or Pearson's chi-squared test.

### Usage

    drawVolcanoPlot(kmers, motif.kmers, motif.rbps,
      significance.threshold = 0.01, show.legend = TRUE)

### Arguments

`kmers` | data frame with the following columns: kmer, adj.p.value, enrichment
`motif.kmers` | set of k-mers that are associated with a certain motif, will be highlighted in volcano plot
`motif.rbps` | name of RNA-binding proteins associated with highlighted k-mers (character vector of length 1)
`significance.threshold` | p-value threshold for significance, e.g., `0.05` or `0.01`
`show.legend` | whether or not a legend should be shown

### Value

volcano plot

### See Also

Other TSMA functions: `runKmerTSMA`, `runMatrixTSMA`

Other k-mer functions: `calculateKmerEnrichment`, `checkKmers`, `computeKmerEnrichment`, `empiricalEnrichmentMeanCDF`, `generateKmers`, `generatePermutedEnrichments`, `homopolymerCorrection`, `permTestGeometricMean`, `runKmerSPMA`, `runKmerTSMA`

### Examples

    motif <- getMotifById("951_12324455")
    drawVolcanoPlot(transite:::kmers.enrichment, motifHexamers(motif[[1]]),
      motifRbps(motif[[1]]))

    ## Not run:
    foreground.set <- c("UGUGGG", "GUGGGG", "GUGUGG", "UGUGGU")
    background.set <- unique(c(foreground.set, c(
      "CAACAGCCUUAAUU", "CAGUCAAGACUCC", "CUUUGGGGAAU",
      "UCAUUUUAUUAAA", "AAUUGGUGUCUGGAUACUUCCCUGUACAU",
      "AUCAAAUUA", "AGAU", "GACACUUAAAGAUCCU",
      "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA",
      "AUAGAC", "AGUUC", "CCAGUAA",
      "CCACACAC", "CUCAUUGGAG", "ACUUUCCCACA", "CAGGUCAGCA",
      "CCACACCAG", "CCACACAUCAGU", "CACACACUCC", "CAGCCCCCCACAGGCA"
    )))

    motif <- getMotifById("M178_0.6")
    results <- runKmerTSMA(list(foreground.set), background.set,
                           motifs = motif)
    drawVolcanoPlot(results[[1]]$motif.kmers.dfs[[1]],
        motifHexamers(motif[[1]]), "test RBP")
    ## End(Not run)

[Package transite version 1.2.1 Index]