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Default parameters for DSB ADT normalisation

params_sc_dsb.Rd

Default parameters for DSB ADT normalisation

Usage

params_sc_dsb(
  denoise_counts = TRUE,
  use_isotype_controls = TRUE,
  pseudocount = 10,
  quantile_low = NULL,
  quantile_high = NULL
)

Arguments

denoise_counts

Boolean. Run Step II (cell-to-cell technical noise removal). Defaults to TRUE.

use_isotype_controls

Boolean. Include isotype controls in the noise matrix in Step II. Requires isotype_indices to be passed at call time. Defaults to TRUE.

pseudocount

Numeric. Pseudocount added before the log transform. The DSB paper recommends 10 with empty droplets and 1 without. Defaults to 10.0.

quantile_low

Numeric or NULL. Optional numeric in [0, 1). Lower quantile for per-protein output clipping. If NULL (and quantile_high is also NULL), no clipping is applied. Defaults to NULL.

quantile_high

Numeric or NULL. Optional numeric in (0, 1]. Upper quantile for per-protein output clipping. If NULL (and quantile_low is also NULL), no clipping is applied. Defaults to NULL.

Value

A named list with the following elements:

  • denoise_counts - Boolean. Run Step II (cell-to-cell technical noise removal). Defaults to TRUE.

  • use_isotype_controls - Boolean. Include isotype controls in the noise matrix in Step II. Requires isotype_indices to be passed at call time. Defaults to TRUE.

  • pseudocount - Numeric. Pseudocount added before the log transform. The DSB paper recommends 10 with empty droplets and 1 without. Defaults to 10.0.

  • quantile_low - Numeric or NULL. Optional numeric in [0, 1). Lower quantile for per-protein output clipping. If NULL (and quantile_high is also NULL), no clipping is applied. Defaults to NULL.

  • quantile_high - Numeric or NULL. Optional numeric in (0, 1]. Upper quantile for per-protein output clipping. If NULL (and quantile_low is also NULL), no clipping is applied. Defaults to NULL.

[0, 1). Lower quantile for per-protein output clipping. If NULL(andquantile_highis alsoNULL), no clipping is applied. Defaults to NULL. \item quantile_high - Numeric or NULL. Optional numeric in (0, 1]: R:0,%201)%60.%20Lower%0A%20quantile%20for%20per-protein%20output%20clipping.%20If%20%60NULL%60%20(and%20%60quantile_high%60%20is%0A%20also%20%60NULL%60),%20no%20clipping%20is%20applied.%20Defaults%20to%20%60NULL%60.%0A%20%5C%5Citem%20quantile_high%20-%20Numeric%20or%20%60NULL%60.%20Optional%20numeric%20in%20%60(0,%201