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", weight = "score", BPPARAM = bpparam() )
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 (columns) |
fraction |
a character (1), info on reads (which read length, or which type (RNA seq)) (row names) |
weight |
(default: 'score'), if defined a character name of valid meta column in subject. GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times. ORFik .bedo files, contains a score column like this. As do CAGEr CAGE files and many other package formats. You can also assign a score column manually. |
BPPARAM |
how many cores/threads to use? default: bpparam() |
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