makewindows: Split Gene Annotations into Fixed-Size Windows

In tepr: Transcription Elongation Profiling

Split Gene Annotations into Fixed-Size Windows

Description

This functions uses the annotations filtered from gencode (see retrieveanno). It removes any ensembl names containing "PAR_Y". It filters out intervals smaller than windsize and splits each transcript into "windsize" windows.

Usage

makewindows(allannobed, windsize, nbcputrans = 1, verbose = TRUE,
   saveobjectpath = NA, showtime = FALSE)

Arguments

allannobed	A data frame which is the result of 'retrieveanno'.
windsize	An integer specifying the number of windows into which each gene annotation should be divided.
nbcputrans	Number of CPU cores to use for transcript-level operations. Defaults to 1.
verbose	A logical value indicating whether to display progress messages. Defaults to 'TRUE'.
saveobjectpath	A character string specifying the directory path where the output object should be saved as an '.rds' file. If 'NA', the object is not saved. Defaults to 'NA'.
showtime	A logical value indicating whether to display the runtime of the function. Defaults to 'FALSE'.

Details

The function filters out annotations with intervals smaller than the specified number of windows ('windsize'). It uses parallel processing to enhance performance when splitting transcripts into fixed-size windows. The result includes metadata for each window, such as its chromosome, start and end coordinates, associated gene, and the window number.

Intermediate functions, such as '.computewindflist' and '.divideannoinwindows', handle computation and validation of windows. Gene intervals with the "PAR_Y" tag are excluded from the analysis.

Value

A data frame containing the split windows for each gene annotation. The output includes fields such as 'biotype', 'chr', 'coor1', 'coor2', 'transcript', 'gene', 'strand', and 'window'.

See Also

[retrieveanno]

Examples

exptabpath <- system.file("extdata", "exptab-preprocessing.csv", package="tepr")
gencodepath <- system.file("extdata", "gencode-chr13.gtf", package = "tepr")
windsize <- 200

## Necessary result to call makewindows
allannobed <- retrieveanno(exptabpath, gencodepath, verbose = FALSE)

## Calling makewindows
allwindowsbed <- makewindows(allannobed, windsize, verbose = FALSE)

tepr documentation built on June 8, 2025, 10:46 a.m.