fastqcr 0.1.1 2018-12-06

New features

New functions added to read and plot a collection of samples together:

When possible, the data from multiple samples are overlayed on a single graph and otherwise on multiple facets (when there is more than one line in a one sample plot). As with plotting the single file modules, the function qc_plot_collection() dispatches on the appropriate class qc_read_collection() and calls the internals corresponding to the input of the argument modules.

Bug fixes

Minor changes

  • New argument fastqc.path added to the function fastqc().

Bug fixes

fastqcr 0.1.0 2017-04-11

Bug fixes

New features

  • fastqc_install(): Install the latest version of FastQC tool on Unix systems (MAC OSX and Linux)

  • fastqc(): Run the FastQC tool from R.

  • qc <- qc_aggregate(): Aggregate multiple FastQC reports into a data frame.

  • summary(qc): Generates a summary of qc_aggregate.

  • qc_stats(qc): General statistics of FastQC reports.

  • qc_fails(qc): Displays samples or modules that failed.

  • qc_warns(qc): Displays samples or modules that warned.

  • qc_problems(qc, “sample”): Union of qc_fails() and qc_warns(). Display which samples or modules that failed or warned.

  • qc_read(): Read FastQC data into R.

  • qc_plot(qc): Plot FastQC data

  • qc_report(): Create an HTML file containing FastQC reports of one or multiple files. Inputs can be either a directory containing multiple FastQC reports or a single sample FastQC report.

  • qc_unzip(): Unzip all zipped files in the qc.dir directory.