Blondal hemolysis index (log miR-451a - log miR-23a-3p) — hemolysis_index

Computes the eLife-14 Blondal-style hemolysis index on a log-abundance matrix as \(\log(\mathrm{miR\text{-}451a}) - \log(\mathrm{miR\text{-}23a\text{-}3p})\). Both anchor features must be present (canonical names hsa-miR-451a / hsa-miR-23a-3p, or the corresponding MIMAT accessions MIMAT0001631 / MIMAT0000078); otherwise NULL is returned and the caller should treat the cell as not hemolysis-correctable. This is the convention the single-sample pipeline uses to feed fit_hemolysis_rr / apply_hemolysis_rr.

Usage

hemolysis_index_blondal(X_log)

Arguments

X_log: Numeric matrix (samples x features) on log-abundance scale. Column names must be canonical mature-miRNA names (post-resolver) or MIMAT accessions.

Value

Numeric vector of length nrow(X_log), or NULL if either anchor feature is missing from colnames(X_log).

References

Blondal T, Jensby Nielsen S, Baker A, Andreasen D, Mouritzen P, Wrang Teilum M, Dahlsveen IK. (2013) Assessing sample and miRNA profile quality in serum and plasma or other biofluids. Methods 59(1): S1-S6.

Examples

X_log <- matrix(c(8, 6, 4, 12, 5, 7, 3, 11), nrow = 2,
                dimnames = list(NULL,
                                c("hsa-miR-451a", "hsa-miR-23a-3p",
                                  "hsa-miR-1", "hsa-miR-2")))
hemolysis_index_blondal(X_log)
#> [1]  4 -6