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 1.2.0 Index]