QCplots: Correlation and coverage plots for ORFikQC

In ORFik: Open Reading Frames in Genomics

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 = paste0(dirname(df$filepath[1]), "/QC_STATS/"),
  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: paste0(dirname(df$filepath[1]), "/QC_STATS/")
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers

Details

Is part of QCreport

Value

invisible(NULL) (objects stored to disc)

See Also

Other QC report: QCreport(), QCstats()

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