select() in place of the deprecated select_() function in qc_aggregate() and qc_problems() (#24)arrange() and group_by() in place of the deprecated arrange_() and group_by()_ functions in qc_problems()qc_read_collection() and qc_plot_collection() examples reduced to less than 5 secondsfill) in left_join() from qc_aggregate() function (#23)New functions added to read and plot a collection of samples together:
qc_read_collection() (@MahShaaban , #4)qc_plot_collection() (@MahShaaban , #4)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.
fastqc.path added to the function fastqc().qc_report() handles better relative paths to FastQC zipfiles (@ACharbonneau, #1)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.