Wraps nondetects::qpcrImpute for Ct-scale qPCR expression matrices.
Falls back to LOD imputation (qpcr_nondetect_lod_fallback)
when either nondetects or HTqPCR is unavailable, or when
the Bayesian fit fails. Sets nondetect_method and
n_imputed attributes on the returned matrix.
Usage
qpcr_nondetect_impute(expr_mat, log_handler = message)
Arguments
- expr_mat
Numeric matrix (features-by-samples) of Ct values; NAs
represent non-detects.
- log_handler
Function used to emit progress messages.
Default message.
Value
Matrix of the same shape as expr_mat with non-detects
imputed. Carries attributes nondetect_method (one of
"nondetects_qpcrImpute", "lod_fallback",
"none_needed") and n_imputed (integer count of
imputed cells).
Examples
if (FALSE) { # \dontrun{
m <- matrix(c(20, NA, 25, 30, NA, NA), nrow = 2,
dimnames = list(c("miR-1", "miR-2"), c("S1", "S2", "S3")))
qpcr_nondetect_impute(m)
} # }