tepr (version 1.1.14)

createtablescores: 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)

Value

A data frame containing the unified table of scores.

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.

See Also

[blacklisthighmap]

Examples

# \donttest{
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)# }