splitIn3Tx {ORFik}R Documentation

Create binned coverage of transcripts, split into the 3 parts.

Description

The 3 parts of transcripts are the leaders, the cds' and trailers. Per transcript part, bin them all to windowSize (default 100), and make a data.table, rows are positions, useful for plotting with ORFik and ggplot2.

Usage

splitIn3Tx(leaders, cds, trailers, reads, windowSize = 100, fraction = "1")

Arguments

leaders

a GRangesList of leaders (5' UTRs)

cds

a GRangesList of coding sequences

trailers

a GRangesList of trailers (3' UTRs)

reads

GRanges or GAlignment of reads

windowSize

an integer (100), size of windows

fraction

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

Value

a data.table with columns position, score


[Package ORFik version 1.6.9 Index]