Z-score a filtered expression matrix for CLAMP

Source: R/utils.R

Centers each gene to mean 0 and scales to unit variance.

zscoreCLAMP(Y_filtered, rowStats)

Arguments

Y_filtered

Numeric matrix (genes x samples) returned by preprocessCLAMP

rowStats

Data frame with numeric columns mean and variance, row-named to match rownames(Y_filtered)

Value

Numeric matrix of the same dimensions as Y_filtered, with each row centered and scaled.

Examples

# simple 2 genes x 3 samples matrix
Y <- matrix(
    c(
        2, 4, 6, # gene1 counts
        8, 10, 12 # gene2 counts
    ),
    nrow = 2, byrow = TRUE,
    dimnames = list(c("gene1", "gene2"), paste0("sample", seq_len(3)))
)

# compute per‐gene mean and variance
rowStats <- data.frame(
    mean = rowMeans(Y),
    variance = apply(Y, 1, var),
    row.names = rownames(Y)
)

# z‐score each row
Y_z <- zscoreCLAMP(Y, rowStats)