QCplots: Correlation and coverage plots for ORFikQC

In JokingHero/ORFik: Open Reading Frames in Genomics

Correlation and coverage plots for ORFikQC

Description

Correlation plots default to mRNA covering reads. Meta plots defaults to leader, cds, trailer.
Output will be stored in same folder as the libraries in df.
Correlation plots will be fpkm correlation and log2(fpkm + 1) correlation between samples.

Usage

QCplots(
  df,
  region = "mrna",
  stats_folder = QCfolder(df),
  plot.ext = ".pdf",
  complex.correlation.plots = TRUE,
  library.names = bamVarName(df),
  force = TRUE,
  BPPARAM
)

Arguments

df	an ORFik experiment
region	a character (default: mrna), make raw count matrices of whole mrnas or one of (leaders, cds, trailers)
stats_folder	directory to save, default: QCfolder(df)
plot.ext	character, default: ".pdf". Alternatives: ".png" or ".jpg". Note that in pdf format the complex correlation plots become very slow to load!
complex.correlation.plots	logical, default TRUE. Add in addition to simple correlation plot two computationally heavy dots + correlation plots. Useful for deeper analysis, but takes longer time to run, especially on low-quality gpu computers. Set to FALSE to skip these.
library.names	character vector, names of libraries, default: name_decider(df, naming)
force	logical, default TRUE If TRUE, reload library files even if matching named variables are found in environment used by experiment (see envExp) A simple way to make sure correct libraries are always loaded. FALSE is faster if data is loaded correctly already.
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers. You can also add a time remaining bar, for a more detailed pipeline.

Details

Is part of QCreport

Value

invisible(NULL) (objects stored to disc)

See Also

Other QC report: QCreport(), QCstats()

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