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:
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.