Hi everyone!

I'm trying to read the code of the functions being used in the EdgeR package during RNA-seq normalization and DE analysis. My background in statistics isn't very good and I like reading the code so I understand what is being done while I try to reproduce it step by step. However, as I go in detail in each of the functions used, I got stuck in the C++ function .cxx_ave_log_cpm and I don't know how to access the code inside. The R function that contains this one is the following:

aveLogCPM.default
function (y, lib.size = NULL, offset = NULL, prior.count = 2, 
    dispersion = NULL, weights = NULL, ...) 
{
    y <- as.matrix(y)
    if (nrow(y) == 0L) 
        return(numeric(0))
    if (.isAllZero(y)) {
        if ((is.null(lib.size) || max(lib.size) == 0) && (is.null(offset) || 
            max(offset) == -Inf)) {
            abundance <- rep(-log(nrow(y)), nrow(y))
            return((abundance + log(1e+06))/log(2))
        }
    }
    if (is.null(dispersion)) 
        dispersion <- 0.05
    isna <- is.na(dispersion)
    if (all(isna)) 
        dispersion <- 0.05
    if (any(isna)) 
        dispersion[isna] <- mean(dispersion, na.rm = TRUE)
    dispersion <- .compressDispersions(y, dispersion)
    weights <- .compressWeights(y, weights)
    offset <- .compressOffsets(y, lib.size = lib.size, offset = offset)
    prior.count <- .compressPrior(y, prior.count)
    maxit <- formals(mglmOneGroup)$maxit
    tol <- formals(mglmOneGroup)$tol
    ab <- .Call(.cxx_ave_log_cpm, y, offset, prior.count, dispersion, ## <----- Here is where the C++ function is being called
        weights, maxit, tol)
    return(ab)
}

This function is being called inside the aveLogCPM.default inside the aveLogCPM.DGEList function.

I'm using:

R version 4.3.1 (2023-06-16) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.1

edgeR_3.42.4

Thanks for all your help! This is my first post in Bioconductor support group so please forgive me if I forgot to include any other information you believe might be needed.

Best,

Josue

You can browse and search all current Bioconductor packages at https://code.bioconductor.org e.g. edgeR can be found at https://code.bioconductor.org/browse/edgeR/

Any C or C++ code should be located in the src directory. In this case I think the code you're looking for can be found in https://code.bioconductor.org/browse/edgeR/blob/devel/src/R_ave_log_cpm.cpp