| 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)