RiboQC.plot: Quality control for pshifted Ribo-seq data

In ORFik: Open Reading Frames in Genomics

Description

Quality control for pshifted Ribo-seq data

Usage

RiboQC.plot(
  df,
  output.dir = file.path(dirname(df$filepath[1]), "QC_STATS/"),
  width = 6.6,
  height = 4.5,
  type = "pshifted",
  weight = "score",
  BPPARAM = BiocParallel::SerialParam(progressbar = TRUE)
)

Arguments

df	an ORFik experiment
output.dir	directory to save plot, default: file.path(dirname(df$filepath[1]), "QC_STATS/"). If NULL will not save.
width	width of plot, default 6.6 (in inches)
height	height of plot, default 4.5 (in inches)
type	type of library loaded, default pshifted, warning if not pshifted might crash if too many read lengths!
weight	which column in reads describe duplicates, default "score".
BPPARAM	how many cores/threads to use? default: bpparam(). To see number of threads used, do bpparam()$workers

Value

ggplot object as a grid

Examples

df <- ORFik.template.experiment()
df <- df[3,] #lets only p-shift RFP sample at index 3
#shiftFootprintsByExperiment(df)
#RiboQC.plot(df)

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