R: Helper function for transcriptWindow

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 1.7.21 Index]