preprocessing: Preprocess Experimental Data for Genomic Analysis

Description

This function orchestrates a pipeline for preprocessing genomic data, including filtering annotations, splitting transcripts into windows, retrieving bedgraph values, and generating a final annotated table.

Usage

preprocessing(exptabpath, gencodepath, windsize, maptrackpath,
blacklistpath, genomename = NA, nbcputrans = 1, finaltabpath = tempdir(),
finaltabname = "anno.tsv", tmpfold = file.path(tempdir(), "tmptepr"),
saveobjectpath = tempdir(), savefinaltable = TRUE, reload = FALSE,
showtime = FALSE, showmemory = FALSE, deletetmp = TRUE, chromtab = NA,
forcechrom = FALSE, verbose = TRUE)

Value

A data frame representing the final table containing transcript information and scores on 'windsize' windows for all experiments defined in the experiment table (exptabpath).

Arguments

exptabpath: Character. Path to the experiment table file.
gencodepath: Character. Path to the Gencode annotation file.
windsize: Integer. Window size for splitting transcripts.
maptrackpath: Character. Path to the mappability track file.
blacklistpath: Character. Path to the blacklist file.
genomename: Character. Name of the genome assembly (e.g., "hg38"). Default is NA. If left to NA, chromtab should be provided.
nbcputrans: Integer. Number of CPUs to use for transcript processing. Default is 1.
finaltabpath: Character. Path where the final annotated table will be saved. Default is tempdir().
finaltabname: Character. Name of the final annotated table file. Default is anno.tsv.
tmpfold: Character. Path to a temporary folder for intermediate files. Default is file.path(tempdir(), "tmptepr").
saveobjectpath: Character. Path to save intermediate objects. Default is tempdir().
savefinaltable: Logical. Whether to save the final table to disk. Default is TRUE.
reload: Logical. Whether to reload intermediate objects if available. Default is FALSE.
showtime: Logical. Whether to display timing information. Default is FALSE.
showmemory: Logical. Whether to display memory usage information. Default is FALSE.
deletetmp: Logical. Whether to delete temporary files after processing. Default is TRUE.
chromtab: A Seqinfo object retrieved with the rtracklayer method SeqinfoForUCSCGenome. If NA, the method is called automatically and the genomename should be provided. Default is NA.
forcechrom: Logical indicating if the presence of non-canonical chromosomes in chromtab (if not NA) should trigger an error. Default is FALSE.
verbose: Logical. Whether to display detailed progress messages. Default is TRUE.

Details

The `preprocessing` function performs several key tasks: 1. Filters Gencode annotations to retrieve "transcript" annotations. 2. Differentiates between protein-coding (MANE_Select) and long non-coding (lncRNA, Ensembl_canonical) transcripts. 3. Splits transcripts into windows of size `windsize`. 4. Processes bedgraph files to retrieve values, exclude blacklisted regions, and retain high-mappability intervals. 5. Generates a final annotated table with scores derived from the above steps.

Temporary files created during processing are optionally deleted at the end.

Examples

Run this code

# \donttest{
## Data
exptabpath <- system.file("extdata", "exptab-preprocessing.csv", package = "tepr")
gencodepath <- system.file("extdata", "gencode-chr13.gtf", package = "tepr")
maptrackpath <- system.file("extdata", "k50.umap.chr13.hg38.0.8.bed",
  package = "tepr")
blacklistpath <- system.file("extdata", "hg38-blacklist-chr13.v2.bed",
    package = "tepr")
windsize <- 200
genomename <- "hg38"

## Copying bedgraphs to the current directory
expdfpre <- read.csv(exptabpath)
bgpathvec <- sapply(expdfpre$path, function(x) system.file("extdata", x,
    package = "tepr"))
expdfpre$path <- bgpathvec
write.csv(expdfpre, file = "exptab-preprocessing.csv", row.names = FALSE,
    quote = FALSE)
exptabpath <- "exptab-preprocessing.csv"

## Testing preprocessing
finaltabtest <- preprocessing(exptabpath, gencodepath, windsize, maptrackpath,
    blacklistpath, genomename = genomename, verbose = FALSE)# }