All functions
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alignToTSS()
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A function to re-align a GRanges object to a provided set of coordinates
(either the TSS column or the TSS.fwd and TSS.rev columns) |
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binWrapper()
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Internal function |
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chunkWrapper()
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Internal function |
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cleanUpDirectory()
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Internal function |
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deconvolveBidirectionalPromoters()
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A function to duplicate bi-directional GRanges into + and - stranded GRanges. |
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generatePeriodicityTrack()
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Core function to generate a track of periodicity strenght of a given
dinucleotide at a given frequency, over a set of chosen GRanges. |
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getChunks()
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Internal function |
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getCovMatrix()
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Internal function |
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getPeriodicity(<DNAStringSet>)
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Function to compute the overall periodicity of a motif over a set of
sequences. |
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getPeriodicity(<GRanges>)
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Core function |
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getPeriodicity()
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Function to compute the overall periodicity of a motif over sequence(s). |
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na.remove()
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A tidyverse-compatible function to remove NAs from a vector |
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na.replace()
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A tidyverse-compatible function to replace NAs in a vector by a given value |
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namedListToLongFormat()
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A function to easily coerce a named list into a long data.frame |
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normalizeHistogram()
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Internal function to normalize a pairwise distance |
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partitionBin()
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Internal function |
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partitionGenome()
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Internal function |
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plotAggregateCoverage(<CompressedRleList>)
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A function to plot aggregated signals (from a CompressedRleList)
over sets of GRanges |
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plotAggregateCoverage()
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A function to plot aggregated signals over sets of GRanges |
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plotAggregateCoverage(<SimpleRleList>)
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A function to plot aggregated signals (from a SimpleRleList)
over sets of GRanges |
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plotAggregateCoverage(<list>)
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A function to plot aggregated signals (from a named list of signal tracks)
over sets of GRanges |
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plotPeriodicityResults()
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Plotting function |
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scaleBigWigs()
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A function to z-score a bigWig track imported by rtracklayer. |
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unlistResults()
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Internal function |
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withSeq()
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Tidyverse-compatible function to add sequence to an existing GRanges |