createtablescores: Create a Unified Table of Scores

In tepr: Transcription Elongation Profiling

Create a Unified Table of Scores

Description

This function processes and combines table scores of each bedgraph and each chromosome stored in the temporary folder into a unified table.

Usage

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.

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.

Value

A data frame containing the unified table of scores.

See Also

[blacklisthighmap]

Examples

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)

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