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", drop.zero.dt = FALSE, 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 ofst, bedoc and .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. |
drop.zero.dt |
logical FALSE, if TRUE and as.data.table is TRUE, remove all 0 count positions. This greatly speeds up and most importantly, greatly reduces memory usage. Will not change any plots, unless 0 positions are used in some sense. (mean, median, zscore coverage will only scale differently) |
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