wavClusteR


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Documentation for package ‘wavClusteR’ version 2.0.0

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wavClusteR-package An R package for the analysis of Next-Generation Sequencing data obtained from PAR-CLIP or other substitution-inducing experimental procedures.
annotateClusters Annotate clusters with respect to transcript features
estimateFDR Estimate False Discovery Rate within the relative substitution frequency support by integrating PAR-CLIP data and RNA-Seq data
exportClusters Export clusters as BED track
exportCoverage Export coverage as BigWig track
exportHighConfSub Export high-confidence substitutions as BED track
exportSequences Export cluster sequences for motif search analysis
filterClusters Merge clusters and compute all relevant cluster statistics
fitMixtureModel Fit a non-parametric mixture model from all identified substitutions
getAllSub Identify all substitutions observed across genomic positions exhibiting a specified minimum coverage
getClusters Identify clusters containing high-confidence substitutions and resolve boundaries at high resolution
getExpInterval Identify the interval of relative substitution frequencies dominated by experimental induction.
getHighConfSub Classify substitutions based on identified RSF interval and return high confidence transitions
getMetaCoverage Compute and plot distribution of average coverage or relative log-odds as metagene profile using identified clusters
getMetaGene Compute and plot metagene profile using identified clusters
getMetaTSS Compute and plot read densities in genomic regions around transcription start sites
model Components of the non-parametric mixture moodel fitted on Ago2 PAR-CLIP data
plotSizeDistribution Plot the distribution of cluster sizes
plotStatistics Pairs plot visualization of clusters statistics
plotSubstitutions Barplot visualization of the number of genomic positions exhibiting a given substitution and, if model provided, additional diagnostic plots.
readSortedBam Load a sorted BAM file
wavClusteR An R package for the analysis of Next-Generation Sequencing data obtained from PAR-CLIP or other substitution-inducing experimental procedures.