countna: Count NA values per transcript and condition

In tepr: Transcription Elongation Profiling

Count NA values per transcript and condition

Description

This function takes a list of expression data frames, a condition information data frame, and counts the number of NA values for each transcript based on strand and condition. NA represent missing scores that were filtered out from the black list and mappability track. The function operates in parallel on transcripts to speed up the process using multiple CPU cores.

Usage

countna(allexprsdfs, expdf, nbcpu = 1, showtime = FALSE, verbose = TRUE)

Arguments

allexprsdfs	A list of data frames containing expression data. The first element is assumed to be the main table. The second element is a vector of transcript names that passed the filtering of 'averageandfilterexprs'.
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 on transcripts. The number of transcripts is equal to the number of lines provided as input of 'averageandfilterexprs'. 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, along with its associated gene, strand, and the count of NA values.

See Also

[averageandfilterexprs]

Examples

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

## Calculating averageandfilterexprs to call countNA
expdf <- read.csv(exppath)
transdf <- read.delim(transpath, header = FALSE)
avfilttest <- averageandfilterexprs(expdf, transdf, expthres,
        showtime = FALSE, verbose = FALSE)

## Testing countna
res <- countna(avfilttest, expdf, nbcpu = 1, verbose = FALSE)

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