tepr (version 1.1.14)

allauc: Calculate Area Under Curve (AUC) and Differences of AUC for Transcript Data

Description

This function computes the Area Under Curve (AUC) and the differences of AUC between two conditions for a list of transcript data. It supports parallel computation for efficiency. If only one condition is given, the differences are not computed.

Usage

allauc(bytranslistmean, expdf, nbwindows, nbcpu = 1,
 controlcondname = "ctrl", stresscondname = "HS", showtime = FALSE,
 verbose = TRUE)

Value

A data frame containing the AUC and dAUC results for each transcript, along with associated statistical information.

Arguments

bytranslistmean

A list of data frames, each containing transcript level data with mean values for one or more conditions.

expdf

A data frame containing experiment data that should have columns named 'condition', 'replicate', 'strand', and 'path'.

nbwindows

An integer specifying the number of windows to consider for AUC calculations.

nbcpu

An integer specifying the number of CPU cores to use for parallel processing on bytranslistmean. Defaults to 1.

controlcondname

A string specifying the name of the control condition Defaults to "ctrl".

stresscondname

A string specifying the name of the stress condition. Defaults to "HS".

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 first checks if exactly two conditions are present in `expdf`. If so, it computes the differences in AUC between the two conditions using a Kolmogorov-Smirnov test. It then calculates the AUC for all conditions against a reference line (y=x). Results are merged by transcript and include adjusted p-values.

See Also

[genesECDF]

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)
ecdf <- genesECDF(avfilt, verbose = FALSE)
resecdf <- ecdf[[1]]
nbwindows <- ecdf[[2]]
meandiff <- meandifference(resecdf, expdf, nbwindows,
    verbose = FALSE)
bytranslistmean <- split(meandiff, factor(meandiff$transcript))

## Testing allauc
res <- allauc(bytranslistmean, expdf, nbwindows, verbose = FALSE)