transcriptWindowPer {ORFik}R Documentation

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
)

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

returnCoverage

return data.table with coverage (default: FALSE)

windowSize

size of binned windows, default: 100

Details

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

Value

NULL, or ggplot object if returnPlot is TRUE


[Package ORFik version 1.6.9 Index]