windowPerTranscript {ORFik} | R Documentation |
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.
windowPerTranscript( txdb, reads, splitIn3 = TRUE, windowSize = 100, fraction = "1" )
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)) |
NOTE: All ranges with smaller width than windowSize, will of course be removed. What is the 100th position on a 1 width object ?
a data.table with columns position, score