Plot distribution of QC statistics

This function plots histograms of the various per-read summary statistics calculated by addReadStats.

Usage

plotReadStats(se)

Arguments

se

A RangedSummarizedExperiment, typically generated by addReadStats.

Value

A ggplot object.

Author

Panagiotis Papapasaikas, Charlotte Soneson

Examples

library(SummarizedExperiment)
modbamfile <- system.file("extdata", "6mA_1_10reads.bam",
                          package = "footprintR")
se <- readModBam(bamfile = modbamfile, regions = "chr1:6940000-6955000",
           modbase = "a", verbose = TRUE)
#> extracting base modifications from modBAM files
#>     opening input file /Users/runner/work/_temp/Library/footprintR/extdata/6mA_1_10reads.bam
#>     reading alignments overlapping any of 1 regions
#>     removed 1724 unaligned (e.g. soft-masked) of 25090 called bases
#>     read 3 alignments
#> finding unique genomic positions...
#> collapsed 11300 positions to 4772 unique ones
se <- addReadStats(se)
plotReadStats(se)