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Compute Negative-Binomial residuals

comp_NB_residuals.Rd

Computes the residuals based on the negative binomial model. By default a theta of 100 is used to capture technical variation.

Usage

comp_NB_residuals(mat, theta = 100, clip = FALSE, cutoff = NULL, freq = TRUE)

Arguments

mat

A numerical matrix or coercible to one by `as.matrix()`. Should have row and column names.

theta

Overdispersion parameter. By default set to 100 as described in Lause and Berens, 2021 (see references).

clip

logical. Whether residuals should be clipped if they are higher/lower than a specified cutoff

cutoff

numeric. Residuals that are larger than cutoff or lower than -cutoff are clipped to cutoff.

freq

logical. Whether a table of frequencies (as used in CA) should be used.

Value

A named list. The elements are:

  • "S": standardized residual matrix.

  • "tot": grand total of the original matrix.

  • "rowm": row masses.

  • "colm": column masses.

References

Lause, J., Berens, P. & Kobak, D. Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data. Genome Biol 22, 258 (2021). https://doi.org/10.1186/s13059-021-02451-7