attenuation: Calculate Attenuation from AUC and Other Transcript Features

In tepr: Transcription Elongation Profiling

Calculate Attenuation from AUC and Other Transcript Features

Description

This function computes the attenuation values for each window of each transcript based on the data frames obtained with the functions 'allauc', 'kneeid', and 'countna'.

Usage

attenuation(allaucdf, kneedf, matnatrans, bytranslistmean, expdf, dfmeandiff,
nbcpu = 1, significant = FALSE, replaceval = NA, pval = 0.1,
showtime = FALSE, verbose = TRUE)

Arguments

allaucdf	A data frame containing AUC results for transcripts (see allauc).
kneedf	A data frame containing the inflection points (see kneeid).
matnatrans	A data frame containing the number of missing values per transcript (see countna).
bytranslistmean	A list of data frames with mean values by transcripts.
expdf	A data frame containing experiment data that should have columns named 'condition', 'replicate', 'strand', and 'path'.
dfmeandiff	A data frame containing means and differences in mean values, if more than one condition. (see meandifference).
nbcpu	An integer specifying the number of CPU cores to use for parallel processing. The parallelization is done on bytranslistmean whose number of elements is equal to the number of lines provided as input of 'averageandfilterexprs'. Defaults to 1.
significant	A logical indicating whether to filter out non-significant attenuation values. Defaults to FALSE.
replaceval	A value to replace non-significant attenuation values Defaults to NA.
pval	A numeric value specifying the p-value threshold for significance of the KS test. Defaults to 0.1.
showtime	A logical value indicating if the duration of the function processing should be indicated before ending. Defaults to FALSE.
verbose	A logical value indicating whether to print progress messages Defaults to TRUE.

Details

The function merges several data frames to create a comprehensive dataset for each transcript. It computes mean values for the "up" and "down" segments of the transcript. The direction is determined by comparing the coordinates to the knee values. up = coord < knee and down = coord > knee. The up and down indexes are then retrieved and the attenuation scores are computed as: att <- 100 - downmean / upmean * 100

Value

A data frame containing the computed attenuation values along with associated transcript information.

See Also

[allauc()], [kneeid()], [countna()], [meandifference()]

Examples

exppath <-  system.file("extdata", "exptab.csv", package="tepr")
transpath <- system.file("extdata", "cugusi_6.tsv", package="tepr")
expthres <- 0.1

## Reading tables
expdf <- read.csv(exppath)
transdf <- read.delim(transpath, header = FALSE)

## Computing intermediate steps
avfilt <- averageandfilterexprs(expdf, transdf, expthres,
       showtime = FALSE, verbose = FALSE)
rescountna <- countna(avfilt, expdf, nbcpu = 1, verbose = FALSE)
ecdf <- genesECDF(avfilt, expdf, verbose = FALSE)
resecdf <- ecdf[[1]]
nbwindows <- ecdf[[2]]
resmeandiff <- meandifference(resecdf, expdf, nbwindows,
    verbose = FALSE)
bytranslistmean <- split(resmeandiff, factor(resmeandiff$transcript))
resknee <- kneeid(bytranslistmean, expdf, verbose = FALSE)
resauc <- allauc(bytranslistmean, expdf, nbwindows, verbose = FALSE)

## Testing attenuation
resatt <- attenuation(resauc, resknee, rescountna, bytranslistmean, expdf,
        resmeandiff, verbose = FALSE)

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