drawVolcanoPlot {transite} | R Documentation |
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.
drawVolcanoPlot(kmers, motif.kmers, motif.rbps, significance.threshold = 0.01, show.legend = TRUE)
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., |
show.legend |
whether or not a legend should be shown |
volcano plot
Other TSMA functions: runKmerTSMA
,
runMatrixTSMA
Other k-mer functions: calculateKmerEnrichment
,
checkKmers
,
computeKmerEnrichment
,
empiricalEnrichmentMeanCDF
,
generateKmers
,
generatePermutedEnrichments
,
homopolymerCorrection
,
permTestGeometricMean
,
runKmerSPMA
, runKmerTSMA
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)