windowPerTranscript: Get a binned coverage window per transcript
In Roleren/ORFik: Open Reading Frames in Genomics

windowPerTranscript

R Documentation

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. Formats which loads a score column like this: Bigwig, wig, ORFik ofst, collapsed bam, bedoc and .bedo. 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()