preprocessing: Preprocess Experimental Data for Genomic Analysis

In tepr: Transcription Elongation Profiling

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)

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.

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).

See Also

[retrieveanno], [makewindows], [blacklisthighmap], [createtablescores]

Examples

## 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)

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