STAR.multiQC: Create STAR multiQC plot and table

Description Usage Arguments Value See Also

View source: R/STAR_multiQC.R


Takes a folder with multiple files from STAR, and create a multiQC report


STAR.multiQC(folder, type = "aligned")



path to LOGS folder of ORFik STAR runs. Can also be the path to the aligned/ (parent directory of LOGS), then it will move into LOG from there. Only if no files with pattern are found in parent directory. If no LOGS folder is found it can check for a folder /aligned/LOGS/ so to go 2 folders down.


a character path, default "aligned". Which subfolder to check for. If you want log files for contamination do type = "contaminants_depletion"


a data.table with all information from STAR runs, plot and data saved to disc. Named: "/00_STAR_LOG_plot.png" and "/00_STAR_LOG_table.csv"

See Also

Other STAR: STAR.align.folder(), STAR.align.single(), STAR.allsteps.multiQC(), STAR.index(), STAR.install(), STAR.remove.crashed.genome(), getGenomeAndAnnotation(), install.fastp()

ORFik documentation built on March 27, 2021, 6 p.m.