Plot distribution of QC statistics

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

Usage

plotReadStats(
  se,
  readInfoCol = "readInfo",
  qcCol = "QC",
  minQscore = NULL,
  maxEntropy = NULL,
  maxFracLowConf = NULL,
  minReadLength = NULL,
  minAlignedLength = NULL,
  minAlignedFraction = NULL,
  minSNR = NULL
)

Arguments

se

A RangedSummarizedExperiment, typically generated by addReadStats.

readInfoCol

A character scalar providing the name of the column in colData that contains read info. Can be NULL if no such column exists.

qcCol

A character scalar providing the name of the column in colData that contains quality metrics (calculated by calcReadStats). Can be NULL if no such column exists.

minQscore, maxEntropy, maxFracLowConf, minReadLength, minAlignedLength, minAlignedFraction, minSNR

Numeric scalars representing possible threshold values used in filterReads, for illustration in the plot panels.

Value

A ggplot object.

Author

Panagiotis Papapasaikas, Charlotte Soneson, Michael Stadler

Examples

library(SummarizedExperiment)
modbamfiles <- system.file("extdata",
                           c("6mA_1_10reads.bam", "6mA_2_10reads.bam"),
                          package = "footprintR")
se <- readModBam(bamfile = modbamfiles, regions = "chr1:6940000-6955000",
                 modbase = "a", verbose = TRUE,
                 BPPARAM = BiocParallel::SerialParam())
#> ℹ extracting base modifications from modBAM files
#> ⠙ 0.000 Mio. genomic positions processed (0.001 Mio./s) [2ms]

#> ⠙ 0.000 Mio. genomic positions processed (0.001 Mio./s) [2ms]
#> ℹ finding unique genomic positions...
#> ✔ finding unique genomic positions... [31ms]
#> 
#> ⠙ 0.000 Mio. genomic positions processed (0.001 Mio./s) [2ms]

#> ℹ collapsed 17739 positions to 7967 unique ones
#> ✔ collapsed 17739 positions to 7967 unique ones [213ms]
#> 
#> ⠙ 0.000 Mio. genomic positions processed (0.001 Mio./s) [2ms]

se <- addReadStats(se, BPPARAM = BiocParallel::SerialParam())
#> Warning: Too few points to estimate noise floor (1); raw noise variances are used.
#> Warning: Too few points to estimate noise floor (0); raw noise variances are used.
plotReadStats(se)