# Create a Unified Table of Scores This function processes and combines table scores of each bedgraph and each chromosome stored in the temporary folder into a unified table. ```r createtablescores(tmpfold, exptabpath, showmemory = FALSE, showtime = FALSE, savefinaltable = TRUE, finaltabpath = tempdir(), finaltabname = "anno.tsv", verbose) ``` ## Arguments - `tmpfold`: A string specifying the temporary folder containing the score files created with the function 'blacklisthighmap'. - `exptabpath`: Path to the experiment table file containing a table with columns named 'condition', 'replicate', 'strand', and 'path'. - `showmemory`: Logical; if `TRUE`, memory usage is printed during processing. Default is `FALSE`. - `showtime`: Logical; if `TRUE`, the execution time of the function is printed. Default is `FALSE`. - `savefinaltable`: Logical; if `TRUE`, the resulting table is saved to disk. Default is `TRUE`. - `finaltabpath`: A string specifying the directory where the final table should be saved. Default is `tempdir()`. - `finaltabname`: A string specifying the name of the final table file. Default is `"anno.tsv"`. - `verbose`: Logical; if `TRUE`, detailed messages are printed during execution. ## Returns A data frame containing the unified table of scores. ## Details This function first merges files belonging to the same experiment and direction. These files are combined into a single table providing two columns per experiment. The first gives the name of the experiment and the second the scores. The resulting table also includes annotations for each transcript. ## Examples ```r 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") tmpfoldpath <- file.path(tempdir(), "tmptepr") windsize <- 200 genomename <- "hg38" chromtabtest <- rtracklayer::SeqinfoForUCSCGenome(genomename) allchromvec <- GenomeInfoDb::seqnames(chromtabtest) chromtabtest <- chromtabtest[allchromvec[which(allchromvec == "chr13")], ] ## 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" ## Necessary result to call createtablescores allannobed <- retrieveanno(exptabpath, gencodepath, verbose = FALSE) allwindowsbed <- makewindows(allannobed, windsize, verbose = FALSE) blacklisthighmap(maptrackpath, blacklistpath, exptabpath, nbcputrans = 1, allwindowsbed, windsize, genomename = genomename, chromtab = chromtabtest, verbose = FALSE) ## Calling the function to test finaltabtest <- createtablescores(tmpfold = tmpfoldpath, exptabpath, savefinaltable = FALSE, verbose = FALSE) ``` ## See Also [blacklisthighmap]

createtablescores function