windowPerTranscript: Get a binned coverage window per transcript

In Roleren/ORFik: Open Reading Frames in Genomics

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",
  weight = "score",
  drop.zero.dt = FALSE,
  BPPARAM = bpparam()
)

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 (columns). All genes with region smaller than this size are filter out for metacoverage.
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()

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

Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.