Package index • footprintR

Filtering BAM files

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

Reading data into R

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)

Calculating on data in R

calcReadStats() addReadStats(): Calculate or add summary statistics for read-level base modification data

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

Footprint identification

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

Score (differential) modifications genome-wide

quantifyWindowsInRegion(): Generate counts for sequential windows in a single region

getDifferentiallyModifiedWindows(): Analyze counts for sequential windows in a single region

fuseWindows(): Identify regions of interest genome-wide.

scanForHighScoringRegions(): Scan one or more chromosomes for high-scoring regions

Visualization

plotReadStats(): Plot distribution of QC statistics

plotRegion() plotReadsLollipop() plotReadsHeatmap() plotSummaryPointSmooth() plotGenomicRegions(): Plot single-molecule footprinting data for a single genomic region

Helper functions

extractSeqContext(): Extract the sequence context around positions of interest

getAnchorRegions(): Extract data for one or more anchor regions

Nucleosome repeat length (NRL) analysis

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.