Package index • SingleMoleculeGenomicsIO

All functions

addSeqContext(): Add sequence context around positions of interest to a SummarizedExperiment
annotateReadSegments(): Add read segment annotation
calcReadStats() addReadStats(): Calculate or add summary statistics for read-level base modification data
checkSEValidity(): Check internal consistency of SummarizedExperiment object
countMismatchStatePairs(): Count pairs of modified bases by distance and modification state for bam files where modifications are indicated by sequence mismatches
countStatePairs(): Count pairs of modified bases by distance and modification state
estimateNoise(): Estimation of noise variance for time series.
estimateSNR(): Estimate a time series Signal to Noise Ratio (SNR) given total and noise variance components and (optionally) a background noise model.
expandSEToBaseSpace(): Expand the rows of a RangedSummarizedExperiment to single base resolution.
extractSeqContext(): Extract the sequence context around positions of interest
filterPositions(): Filter positions
filterReads(): Filter reads
filterReadsModBam(): Write bam records from infile to outfile if they pass filter criteria.
flattenReadLevelAssay(): Summarize a read-level object to sample-level
getReadLevelAssayNames(): Get names of assays containing read-level data
getReadLevelColDataNames(): Get names of colData columns containing read-level data
plotReadStats(): Plot distribution of QC statistics
readBedMethyl(): Read collapsed single-molecule footprinting data from a bedMethyl file
readMismatchBam(): Read base modifications from "C-to-T" bam file(s)
readModBam(): Read base modifications from bam file(s)
readModkitExtract(): Read modkit extract file(s)
refargToDNAStringSet(): Convert a supported reference sequence argument to a DNAStringSet
regionStringToGRanges(): Convert character region(s) to a GRanges object
regroupReads() regroupReadsByColData(): Regroup reads
removeAllNAReads(): Remove all-NA reads
sampleEntropy(): Sample Entropy of Time series signal
subsetReads(): Subset the reads from read-level assays