STAR.multiQC: Create STAR multiQC plot and table

In Roleren/ORFik: Open Reading Frames in Genomics

Create STAR multiQC plot and table

Description

Takes a folder with multiple Log.final.out files from STAR, and create a multiQC report

Usage

STAR.multiQC(
  folder,
  type = "aligned",
  plot.ext = ".pdf",
  log_files = dir(folder, "Log.final.out", full.names = TRUE),
  simplified_table = TRUE
)

Arguments

folder	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 Log.final.out 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.
type	a character path, default "aligned". Which subfolder to check for. If you want log files for contamination do type = "contaminants_depletion"
plot.ext	character, default ".pdf". Which format to save QC plot. Alternative: ".png".
log_files	character, path to "Log.final.out" STAR files, default: dir(folder, "Log.final.out", full.names = TRUE)
simplified_table	logical, default TRUE. Subset columns, to the most important ones.

Value

a data.table with all information from STAR runs, plot and data saved to disc. Named: "/00_STAR_LOG_plot.pdf" 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()

Examples

#' @examples
process_dir <- system.file("extdata/test_processing/", package = "ORFik")
STAR.multiQC(process_dir)

Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.