averageandfilterexprs: Calculate Average Expression and Filter Transcript Data

In tepr: Transcription Elongation Profiling

Calculate Average Expression and Filter Transcript Data

Description

This function calculates the average expression levels for transcripts from a provided expression data frame and filters out transcripts based on a specified expression threshold. The function also renames the columns in the output data frame to include mean expression values.

Usage

averageandfilterexprs(expdf, alldf, expthres, showtime = 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.
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

If no transcript is selected as expressed, the function throws an error.

Value

A list containing:

maintable	The original data frame containing all transcript data.
exptranstab	A character vector of transcripts that meet the filtering criteria.

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)

## Testing averageandfilterexprs
resavfilt <- averageandfilterexprs(expdf, transdf, expthres,
       showtime = FALSE, verbose = FALSE)

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