transcriptWindowPer: Helper function for transcriptWindow

Description Usage Arguments Details Value See Also

View source: R/experiment_plots.R

Description

Make 100 bases size meta window for one library in experiment

Usage

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transcriptWindowPer(
  leaders,
  cds,
  trailers,
  df,
  outdir = NULL,
  scores = c("sum", "zscore"),
  reads,
  returnCoverage = FALSE,
  windowSize = 100,
  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", "zscore")), 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

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: transcriptWindow1(), transcriptWindow()


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