teprmulti: Perform tepr differential nascent rna-seq analysis for...
In tepr: Transcription Elongation Profiling

teprmulti

R Documentation

Perform tepr differential nascent rna-seq analysis for multiple conditions

Description

This function performs tepr differential nascent RNA-seq analysis for multiple conditions. It iterates over all pairwise comparisons of conditions within the experiment table and calls the 'tepr' function for each pair.

Usage

teprmulti(expdf, alldf, expthres, nbcpu = 1, rounding = 10,
 dontcompare = NULL, replaceval = NA, pval = 0.1, significant = FALSE,
 windsizethres = 50, countnathres = 20, pvaltheorythres = 0.1,
 meancond1thres = 0.5, meancond2thres = 0.5,
 auccond1threshigher = -10, auccond1threslower = 15, auccond2thres = 15,
 attenuatedpvalksthres = 2, outgrouppvalksthres = 0.2,
 saveobjectpath = NA, reload = FALSE, showtime = FALSE, showmemory = FALSE,
 verbose = TRUE)

Arguments

`expdf`	A data frame containing experiment data that should have columns named 'condition', 'replicate', 'strand', and 'path'.
`alldf`	A data frame containing all transcript-related information, including biotype, chromosome, coordinates, transcript, gene, strand, window, ID and scores retrieved from the bedgraph files.
`expthres`	A numeric value specifying the expression threshold. Transcripts with average expression values below this threshold will be filtered out from the returned transcript vector.
`nbcpu`	An integer specifying the number of CPU cores to use for parallel computation on transcripts. Defaults to `1`.
`rounding`	An integer specifying the rounding factor for computing ECDF. Default is `10`.
`dontcompare`	An optional vector specifying conditions to exclude from the comparison. It should use condition names from expdf and follow the pattern `cond1_vs_cond2`. Defaults to `NULL`.
`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`.
`significant`	A logical indicating whether to filter out non-significant attenuation values. Defaults to `FALSE`.
`windsizethres`	A numeric threshold for the minimum window size. Default is 50.
`countnathres`	A numeric threshold for the maximum number of missing data points for an experiment (NA values). Default is 20.
`pvaltheorythres`	A numeric threshold for the minimum p-value used to define the universe of genes. Default is 0.1.
`meancond1thres`	A numeric threshold for the minimum mean transcription value in the first condition of each comparison. Default is 0.5.
`meancond2thres`	A numeric threshold for the minimum mean transcription value in the second condition of each comparison. Default is 0.5.
`auccond1threshigher`	A numeric threshold for the lower bound of the first condition AUC value in the outgroup classification. Default is -10.
`auccond1threslower`	A numeric threshold for the upper bound of the first condition AUC value in the outgroup classification. Default is 15.
`auccond2thres`	A numeric threshold for the minimum second condition AUC value used to classify attenuated genes. Default is 15.
`attenuatedpvalksthres`	A numeric threshold for the negative log10 of the p-value (from KS test) for defining attenuated genes. Default is 2.
`outgrouppvalksthres`	A numeric threshold for the maximum KS p-value used to define the outgroup. Default is 0.2.
`saveobjectpath`	A character string specifying the path to save the object of the results for each comparison. The file names are defined with the 'condition' column of expdf. Defaults to `NA`.
`reload`	Logical. If 'TRUE', reloads existing saved objects to avoid recomputation. Default is 'FALSE'. If the function failed during object saving, make sure to delete the corresponding object.
`showtime`	A logical value indicating if the duration of the function processing should be indicated before ending. Defaults to `FALSE`.
`showmemory`	A logical value indicating if memory usage should be printed during the execution. Defaults to `FALSE`.
`verbose`	A logical flag indicating whether to print progress messages. Defaults to `TRUE`.

Value

A list of lists. Each inner list corresponds to a pairwise comparison and contains two data frames: - 'resmeandiff_<comparison>': Results from the 'meandifference' function for the specific comparison. - 'resunigroupatt_<comparison>': Results from the 'universegroup' function for the specific comparison.

Examples

## Supposing the data have more than one condition
## Not run: 
  exptabpath <- "exp.csv"
  alldfpath <- "result-preprocessing.tsv"
  expdf <- read.csv(exptabpath)
  alldf <- read.delim(alldfpath, header = FALSE)
  expthres <- 0.1
  reslist <- teprmulti(expdf, alldf, expthres)
## End(Not run)

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