Set of tools to identify periodic occurrences of k-mers in DNA sequences


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Documentation for package ‘periodicDNA’ version 1.0.0

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ce11_all_REs ce11_all_REs
ce11_ATACseq ce11_ATACseq
ce11_proms ce11_proms
ce11_proms_seqs ce11_proms_seqs
ce11_TSSs ce11_TSSs
ce11_WW_10bp ce11_WW_10bp
getPeriodicity A function to compute k-mer periodicity in sequence(s).
getPeriodicity.DNAString A function to compute k-mer periodicity in sequence(s).
getPeriodicity.DNAStringSet A function to compute k-mer periodicity in sequence(s).
getPeriodicity.GRanges A function to compute k-mer periodicity in sequence(s).
getPeriodicityTrack Function to generate a k-mer periodicity track
getPeriodicityWithIterations A function to compute PSDs with iterations
getPeriodicityWithIterations.DNAStringSet A function to compute PSDs with iterations
getPeriodicityWithIterations.GRanges A function to compute PSDs with iterations
plotAggregateCoverage A function to plot aggregated signals over sets of GRanges
plotAggregateCoverage.CompressedRleList A function to plot aggregated signals over sets of GRanges
plotAggregateCoverage.list A function to plot aggregated signals over sets of GRanges
plotAggregateCoverage.SimpleRleList A function to plot aggregated signals over sets of GRanges
plotPeriodicityResults Plot the output of getPeriodicity()
setUpBPPARAM setUpBPPARAM
theme_ggplot2 Personal ggplot2 theming function, adapted from roboto-condensed at https://github.com/hrbrmstr/hrbrthemes/