Perform essential preprocessing steps for raw RNA-seq counts

The preprocess_rna_seq_data() function performs essential preprocessing steps for raw RNA-seq counts. This includes creating a DGEList object, normalizing the counts using the default TMM (Trimmed Mean of M-values) normalization via the edgeR::calcNormFactors function, and applying the voom transformation from the limma package to obtain log-transformed counts per million (logCPM) with associated precision weights. If you require a different normalization method, you can supply your own custom normalization function.

Usage

preprocess_rna_seq_data(splineomics, normalize_func = NULL, verbose = TRUE)

Arguments

splineomics

SplineOmics: An S3 object of class SplineOmics that must contain the following elements:

data: matrix A matrix of the omics dataset, with feature names optionally as row headers (genes as rows, samples as columns).
meta: data.frame A dataframe containing metadata corresponding to the data. The dataframe must include a 'Time' column and a column specified by the condition.
design: character(1) A character string representing the design formula for the limma analysis (e.g., '~ 1 + Phase*X + Reactor').
spline_params: list A list of spline parameters used in the analysis. This can include:
- spline_type: character(1) A character string specifying the type of spline. Must be either 'n' for natural cubic splines or 'b' for B-splines.
- dof: integer(1) An integer specifying the degrees of freedom. Required for both natural cubic splines and B-splines.
- degree: integer(1) An integer specifying the degree of the spline (for B-splines only).
use_array_weights: logical(1) | NULL Boolean flag indicating if the robust fit strategy to deal with heteroscedasticity should be used or not. If set to NULL, then this is handled implicitly based on the result of the Levene test. If this test is significant for at least 10% of the features, then the robust strategy is used. The robust strategy uses the function voomWithQualityWeights for RNA-seq data instead of the normal voom function. For other, non-count-based data, the function limma::arrayWeights is used instead, combined with setting the robust argument to TRUE for the limma::eBayes function. In summary, the strategy employed by those functions is to downweight samples with higher variance. This can be necessary, because linear models have the assumption of homoscedasticity, which means that the variance is (approx.) the same across all datapoints where the linear model is fitted. If this is violated, then the resulting p-values cannot be trusted (common statistical wisdom).
bp_cfg: numeric() | NULL A named numeric vector specifying the parallelization configuration, with expected names "n_cores" and "blas_threads".

This controls how many R worker processes (n_cores) and how many BLAS/OpenBLAS threads per process (blas_threads) should be used during parallel computation.

If bp_cfg is NULL, missing, or any of its required fields is NA, both n_cores and blas_threads default to 1. This effectively disables parallelization and avoids oversubscription of CPU threads.

normalize_func

function | NULL: An optional normalization function. If provided, this function will be used to normalize the DGEList object. If not provided, TMM normalization (via edgeR::calcNormFactors) will be used by default. Must take as input the y of: y <- edgeR::DGEList(counts = raw_counts) and output the y with the normalized counts.

verbose

logical(1): Boolean flag controlling the display of messages.

Value

The updaed splineomics object, now containing the voom object, which includes the log2-counts per million (logCPM) matrix and observation-specific weights. Additionally, the splineparams are updated with the identified optimal dof based on LOOCV, when dof = 0L (for auto-dof)

Examples

if (requireNamespace("edgeR", quietly = TRUE) &&
    requireNamespace("limma", quietly = TRUE)) {
    # Toy raw counts: 4 genes x 6 samples (2 conditions x 3 timepoints)
    set.seed(1)
    counts <- matrix(
        rpois(24, lambda = 20),
        nrow = 4, ncol = 6,
        dimnames = list(paste0("g", 1:4), paste0("s", 1:6))
    )

    meta <- data.frame(
        Time = c(0, 1, 2, 0, 1, 2),
        condition = rep(c("WT", "KO"), each = 3),
        row.names = colnames(counts)
    )

    # Simple fixed-effects design (no random effects → uses limma::voom)
    design_str <- "~ 0 + Time + condition"

    # Spline params: natural cubic with fixed dof (avoid auto-dof path)
    sp <- list(
        spline_type = "n", dof = 3L, degree = NA_integer_
    )

    # Build minimal SplineOmics object
    so <- list(
        data = counts,
        meta = meta,
        design = design_str,
        condition = "condition",
        spline_params = sp,
        use_array_weights = FALSE, # skip homoscedasticity auto-check
        bp_cfg = list(n_cores = 1L, blas_threads = 1L)
    )
    class(so) <- "SplineOmics"

    # Run preprocessing (TMM + voom)
    so2 <- preprocess_rna_seq_data(so)

    # Inspect the voom results (logCPM matrix dimensions)
    if (!is.null(so2$rna_seq_data)) {
        dim(so2$rna_seq_data$E)
    }
}
#> Preprocessing RNA-seq data (normalization + voom)...
#> Coefficients not estimable: X3 
#> Warning: Partial NA coefficients for 4 probe(s)
#> Info Finished preprocessing RNA-seq
#>         data in 0.0 minutes
#> [1] 4 6

Usage

Arguments

Value

See also

Examples