NEWS.md

In fastqcr: Quality Control of Sequencing Data

fastqcr 0.1.3

Minor changes

• Using select() in place of the deprecated select_() function in qc_aggregate() and qc_problems() (#24)
• Using arrange() and group_by() in place of the deprecated arrange_() and group_by()_ functions in qc_problems()
• Changing http to https for urls concerning fastc installation and documentation
• qc_read_collection() and qc_plot_collection() examples reduced to less than 5 seconds

Bug fixes

• Remove extra args (fill) in left_join() from qc_aggregate() function (#23)

fastqcr 0.1.2

Bug fixes

• Revert "Fix for readr 1.2.0": readr 1.3.0 changes the skip line behavior to match that of readr 1.1.1, the change in 1.2.0 was determined to be too disruptive (@jimhester, #11).

fastqcr 0.1.1

New features

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.

Bug fixes

• Fix for readr 1.2.0 (@jimhester, #7)

Minor changes

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

Bug fixes

fastqcr 0.1.0

Bug fixes

• Now, qc_report() handles better relative paths to FastQC zipfiles (@ACharbonneau, #1)

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.

fastqcr documentation built on March 7, 2023, 8:16 p.m.