Package index • footprintR

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

addReadStats(): Add a variety of read-level modified basecalling summary statistics to a SummarizedExperiment

addSeqContext(): Add sequence context around positions of interest to a SummarizedExperiment.

addReadsSummary(): Summarize a read-level object to sample-level.

sumOverRegions(): Sum number of modified and total reads for each region.

subsetReads(): Subset the reads from read-level assays.

Visualization

plotReadStats(): Plot distribution of QC statistics

plotRegion(): Plot single-molecule footprinting data for a single genomic region.

Helper functions

calcReadStats(): Calculate a variety of read-level modified basecalling summary statistics

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

modkitExtract(): Call modkit extract to extract read-level base modifications from modBAM files

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.