makewindows: 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)

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`.

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.

Examples

Run this code

# \donttest{
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)# }