windowPerTranscript {ORFik}R Documentation

Get a binned coverage window per transcript

Description

Per transcript (or other regions), bin them all to windowSize (default 100), and make a data.table, rows are positions, useful for plotting with ORFik and ggplot2.

Usage

windowPerTranscript(
  txdb,
  reads,
  splitIn3 = TRUE,
  windowSize = 100,
  fraction = "1"
)

Arguments

txdb

a TxDb object or a path to gtf/gff/db file.

reads

GRanges or GAlignment of reads

splitIn3

a logical(TRUE), split window in 3 (leader, cds, trailer)

windowSize

an integer (100), size of windows

fraction

a character (1), info on reads (which read length, or which type (RNA seq))

Details

NOTE: All ranges with smaller width than windowSize, will of course be removed. What is the 100th position on a 1 width object ?

Value

a data.table with columns position, score


[Package ORFik version 1.6.9 Index]