Package index • footprintR

Filtering BAM files

filterReadsBam(): Write bam records from infile to outfile if they pass filter criteria.

readBedMethyl(): Read collapsed single-molecule footprinting data from a bedMethyl file
readModBam(): Read base modifications from bam file(s)
readModkitExtract(): Read modkit extract file(s)
countStatePairs(): Count pairs of modified bases by distance and modification state

calcReadStats() addReadStats(): Calculate or add summary statistics for read-level base modification data
sampleEntropy(): Sample Entropy of Time series signal
addSeqContext(): Add sequence context around positions of interest to a SummarizedExperiment
flattenReadLevelAssay(): Summarize a read-level object to sample-level
filterPositions(): Filter positions
filterReads(): Filter reads
subsetReads(): Subset the reads from read-level assays
regroupReads() regroupReadsByColData(): Regroup reads

addFootprints() calcFootprintScores() segmentFootprintScores(): Calculate and segment scores for footprints and add them to a SummarizedExeriment

quantifyWindowsInRegion(): Generate counts for sequential windows in a single region
sumNmodNvalid(): Quantify windows by summing across positions in each of Nmod and Nvalid
strandDiffFracMod(): Quantify windows by calculating the difference between modification fractions for the positive and negative strand
phasingScoreFourier(): Quantify windows by calculating a Fourier-transform-based phasing score
estimateNRLwindows(): Quantify windows by estimating nucleosome repeat lengths (NRLs)
estimateNoiseParsWindows(): Estimate a background noise model
estimateSNRwindows(): Quantify footprint coherence in windows by estimating the Signal to Noise Ratio (SNR)
getDifferentiallyModifiedWindows(): Analyze counts for sequential windows in a single region
getDifferentialWindows(): Perform differential analysis on the rows of an assay
getRangesWithAssayValues(): Create a GRanges from a SummarizedExperiment.
processWindowScores(): Process scores of sequential genomic windows.
scanForHighScoringRegions(): Scan one or more chromosomes for high-scoring regions

plotReadStats(): Plot distribution of QC statistics
plotNoisePars(): Plot background noise model fit diagnostics.
plotRegion() plotBigWig() plotReadsLollipop() plotReadsHeatmap() plotSummaryPointSmooth() plotGenomicRegions(): Plot single-molecule footprinting data for a single genomic region

extractSeqContext(): Extract the sequence context around positions of interest
getAnchorRegions(): Extract data for one or more anchor regions

Functions for calculating and visualizing distance distributions between modified bases and estimate NRL.

calcModbaseSpacing(): Calculate distances between modified bases on individual reads
estimateNRL(): Estimate the nucleosome repeat length (NRL) from modified-base distances
plotModbaseSpacing(): Plot annotated distances between modified bases
calcAndCountDist(): Count frequency of differences between values in integer vectors.