Limit-of-detection fallback imputation for qPCR non-detects

Replaces every NA in expr_mat with the supplied lod_ct value (default 40). Used by the single-sample pipeline when Bayesian hierarchical imputation via nondetects is unavailable or fails. Sets nondetect_method = "lod_fallback" and n_imputed attributes.

Usage

qpcr_nondetect_lod_fallback(expr_mat, lod_ct = 40, log_handler = message)

Arguments

expr_mat

Numeric matrix of Ct values; NAs represent non-detects.

lod_ct

Numeric scalar; the Ct value used to impute NAs. Default 40.

log_handler

Function used to emit progress messages. Default message.

Value

Matrix of the same shape as expr_mat, with NAs filled by lod_ct. Carries attributes nondetect_method and n_imputed.

Examples

m <- matrix(c(20, NA, 25, 30, NA, NA), nrow = 2,
            dimnames = list(c("miR-1", "miR-2"), c("S1", "S2", "S3")))
qpcr_nondetect_lod_fallback(m, log_handler = function(...) invisible())
#>       S1 S2 S3
#> miR-1 20 25 40
#> miR-2 40 30 40
#> attr(,"nondetect_method")
#> [1] "lod_fallback"
#> attr(,"n_imputed")
#> [1] 3