transcriptWindowPer: Helper function for transcriptWindow

In Roleren/ORFik: Open Reading Frames in Genomics

Helper function for transcriptWindow

Description

Make 100 bases size meta window for one library in experiment

Usage

transcriptWindowPer(
  leaders,
  cds,
  trailers,
  df,
  outdir = NULL,
  scores = c("sum", "zscore"),
  reads,
  returnCoverage = FALSE,
  windowSize = 100,
  drop.zero.dt = TRUE,
  BPPARAM = bpparam()
)

Arguments

leaders	a GRangesList of leaders (5' UTRs)
cds	a GRangesList of coding sequences
trailers	a GRangesList of trailers (3' UTRs)
df	an ORFik experiment
outdir	directory to save to (default: NULL, no saving)
scores	scoring function (default: c("sum", "transcriptNormalized")), see ?coverageScorings for possible scores.
reads	a GRanges / GAligment object of reads, can also be a list of those.
returnCoverage	return data.table with coverage (default: FALSE)
windowSize	size of binned windows, default: 100
drop.zero.dt	logical FALSE, if TRUE and as.data.table is TRUE, remove all 0 count positions. This greatly speeds up and most importantly, greatly reduces memory usage. Will not change any plots, unless 0 positions are used in some sense. (mean, median, zscore coverage will only scale differently)
BPPARAM	how many cores/threads to use? default: bpparam()

Details

Gives you binned meta coverage plots, either saved seperatly or all in one.

Value

NULL, or ggplot object if returnPlot is TRUE

See Also

Other experiment plots: transcriptWindow(), transcriptWindow1()

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