A General Framework for Quality Control Metrics

About

The qcmetrics package provides a general framework to develope quality control (QC) pipelines for any type of data that can be imported into R. The application of qcmetrics can be schematised in 5 points

  1. Identify a set of quality metrics of interest and implement them and their visualisation method into individual QcMetric instances.
  2. Bundles the QcMetric items into a QcMetrics instance.
  3. Automatically generate reports in pdf of html using the qcReport function using the QcMetrics object of step 2 as input.
  4. Optionally, reports can be customised.
  5. Wrap the above steps into a wrapper function or a new QC package for production use.

QC pipelines and packages will be described and disseminated through the wiki.

Installation

qcmetrics is a Bioconductor package and should in installed with

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("qcmetrics")

Bugs and question

Either file a GitHub issue or use the Bioconductor support forum.