STAR.allsteps.multiQC: Create STAR multiQC plot and table

In JokingHero/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. This is automatically run with STAR.align.folder function.

Usage

STAR.allsteps.multiQC(
  folder,
  steps = "auto",
  plot.ext = ".pdf",
  output.file = file.path(folder, "full_process.csv")
)

Arguments

folder	path to main output folder of STAR run. The folder that contains /aligned/, "/trim/, "contaminants_depletion" etc. To find the LOGS folders in, to use for summarized statistics.
steps	a character, default "auto". Find which steps you did. If manual, a combination of "tr-co-ge". See STAR alignment functions for description.
plot.ext	character, default ".pdf". Which format to save QC plot. Alternative: ".png".
output.file	character, file path, default: file.path(folder, "full_process.csv")

Value

data.table of main statistics, plots 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.index(), STAR.install(), STAR.multiQC(), STAR.remove.crashed.genome(), getGenomeAndAnnotation(), install.fastp()

Examples

process_dir <- system.file("extdata/test_processing/", package = "ORFik")
STAR.allsteps.multiQC(process_dir)
STAR.allsteps.multiQC(process_dir, steps = "tr-ge")

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.