# Preprocess Experimental Data for Genomic Analysis 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. ```r 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`. ## Returns A data frame representing the final table containing transcript information and scores on 'windsize' windows for all experiments defined in the experiment table (exptabpath). ## 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 ```r ## 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) ``` ## See Also [retrieveanno], [makewindows], [blacklisthighmap], [createtablescores]

preprocessing function