Single-sample qPCR non-detect imputation (Module B add-on)

Two qPCR non-detect handlers used by the single-sample pipeline:

• qpcr_nondetect_impute: Bayesian hierarchical imputation via the nondetects Bioconductor package (McCall et al. 2014).

• qpcr_nondetect_lod_fallback: limit-of-detection fallback that fills undetermined Cts with a fixed value (default 40).

Both operate on a features-by-samples Ct matrix. NAs in the input represent undetermined Cts. The Bayesian path requires both nondetects and HTqPCR (Bioconductor); if either is unavailable, the function falls back to LOD imputation with a logged message. This mirrors the single-sample non-detect handling convention.

References

McCall MN, McMurray HR, Land H, Almudevar A. (2014) On non-detects in qPCR data. Bioinformatics 30(16): 2310-2316.