Wrapper function to generate GSVA parameters

Wrapper function to generate GSVA parameters

Usage

params_gsva(
  tau = 1,
  min_size = 5L,
  max_size = 500L,
  max_diff = TRUE,
  abs_rank = FALSE
)

Arguments

tau

Numeric. Tau parameter, usual recommendation is to use 1.0 here. Larger values emphasise the tails more. Defaults to 1.0.

min_size

Integer. Minimum number of genes per gene set. Defaults to 5L.

max_size

Integer. Maximum number of genes per gene set. Defaults to 500L.

max_diff

Boolean. Scoring mode for GSVA, if TRUE = difference; if FALSE = larger absolute value. Defaults to TRUE.

abs_rank

Boolean. If TRUE = pos - neg, FALSE = pos + neg. Defaults to FALSE.

Value

A named list with the following elements:

• tau - Numeric. Tau parameter, usual recommendation is to use 1.0 here. Larger values emphasise the tails more. Defaults to 1.0.

• min_size - Integer. Minimum number of genes per gene set. Defaults to 5L.

• max_size - Integer. Maximum number of genes per gene set. Defaults to 500L.

• max_diff - Boolean. Scoring mode for GSVA, if TRUE = difference; if FALSE = larger absolute value. Defaults to TRUE.

• abs_rank - Boolean. If TRUE = pos - neg, FALSE = pos + neg. Defaults to FALSE.