# Quality Assessment Tools for Oxford Nanopore MinION data

## Documentation for package ‘IONiseR’ version 2.11.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

IONiseR-package | IONiseR: A package for assessing quality of MinION data
baseCalled | Extract baseCalled slot
baseCalled-method | An S4 class for summarised data from a MinION sequencing run
channelActivityPlot | Visualise a specified metric over all channels over time.
channelHeatmap | Create layout plot of flowcell
eventData | Extract eventData slot
eventData-method | An S4 class for summarised data from a MinION sequencing run
Fast5Summary-class | An S4 class for summarised data from a MinION sequencing run
fast5toFastq | Extract FASTQ files from fast5 files
fastq | Extract fastq slot
fastq-method | An S4 class for summarised data from a MinION sequencing run
fastq2D | Extract 2D reads
fastq2D-method | An S4 class for summarised data from a MinION sequencing run
fastqComplement | Extract complement reads
fastqComplement-method | An S4 class for summarised data from a MinION sequencing run
fastqTemplate | Extract template reads
fastqTemplate-method | An S4 class for summarised data from a MinION sequencing run
IONiseR | IONiseR: A package for assessing quality of MinION data
layoutPlot | Create layout plot of flowcell
length-method | An S4 class for summarised data from a MinION sequencing run
muxHeatmap | Create layout plot of flowcell
plotActiveChannels | Plot the number of active channels for each minute of run time
plotBaseProductionRate | Plot the mean rate at which bases are recorded
plotCurrentByTime | View changes in signal against run time.
plotEventRate | Plot the mean rate at which events occur
plotKmerFrequencyCorrelation | Display correlation between pentemer proportions in two time windows
plotReadAccumulation | Plot the accumulation of reads over the duration of the experiment.
plotReadCategoryCounts | Plot the proportion of template, complement and 2D reads found a dataset.
plotReadCategoryQuals | Visualise the mean base quality of each read
plotReadTypeProduction | View changes in signal against run time.
readFast5Log | Read the log entry from a single fast5 file
readFast5Summary | Read summary data from fast5 files.
readInfo | Extract readInfo slot
readInfo-method | An S4 class for summarised data from a MinION sequencing run
[-method | An S4 class for summarised data from a MinION sequencing run