splitIn3Tx: Create binned coverage of transcripts, split into the 3...
In Roleren/ORFik: Open Reading Frames in Genomics

splitIn3Tx

R Documentation

Create binned coverage of transcripts, split into the 3 parts.

Description

The 3 parts of transcripts are the leaders, the cds' and trailers. Per transcript part, bin them all to windowSize (default 100), and make a data.table, rows are positions, useful for plotting with ORFik and ggplot2.

Usage

splitIn3Tx(
  leaders,
  cds,
  trailers,
  reads,
  windowSize = 100,
  fraction = "1",
  weight = "score",
  is.sorted = FALSE,
  drop.zero.dt = FALSE,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

`leaders`	a `GRangesList` of leaders (5' UTRs)
`cds`	a `GRangesList` of coding sequences
`trailers`	a `GRangesList` of trailers (3' UTRs)
`reads`	GRanges or GAlignment of reads
`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.
`is.sorted`	logical (FALSE), is grl sorted. That is + strand groups in increasing ranges (1,2,3), and - strand groups in decreasing ranges (3,2,1)
`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()