kneeid: Identify the Knee and Max ECDF Differences for Each...

In tepr: Transcription Elongation Profiling

Identify the Knee and Max ECDF Differences for Each Transcript

Description

This function identifies the knee point (i.e., point of maximum change) and the maximum difference in the empirical cumulative distribution function (ECDF) for each transcript, across different experimental conditions.

Usage

kneeid(transdflist, expdf, nbcpu = 1, showtime = FALSE, verbose = TRUE)

Arguments

transdflist	A list of data frames where each data frame contains transcript data with ECDF values for each condition.
expdf	A data frame containing experiment data that should have columns named 'condition', 'replicate', 'strand', and 'path'.
nbcpu	An integer specifying the number of CPU cores to use for parallel computation. The parallelization is performed on the elements of transdflist. Defaults to 1.
showtime	A logical value indicating if the duration of the function processing should be indicated before ending. Defaults to FALSE.
verbose	A logical flag indicating whether to print progress messages. Defaults to TRUE.

Value

A data frame where each row corresponds to a transcript and contains the coordinates of the knee point and the maximum ECDF difference for each condition.

Examples

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

## Calculating necessary results
expdf <- read.csv(exppath)
transdf <- read.delim(transpath, header = FALSE)
avfilt <- averageandfilterexprs(expdf, transdf, expthres,
        showtime = FALSE, verbose = FALSE)
ecdf <- genesECDF(avfilt, expdf, verbose = FALSE)
resecdf <- ecdf[[1]]
nbwindows <- ecdf[[2]]
meandiff <- meandifference(resecdf, expdf, nbwindows,
    verbose = FALSE)
bytranslistmean <- split(meandiff, factor(meandiff$transcript))

## Testing kneeid
reskneeid <- kneeid(bytranslistmean, expdf, verbose = FALSE)

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