Gene Set Variation Analysis (GSVA) Scorer

This scorer returns the *gene set variation analysis (GSVA)* score(s). See the **Details** section below for further information.

Usage

gsvaScorer(
  x,
  i = NULL,
  na.rm = TRUE,
  transform.fun = NULL,
  transform.args = list(),
  transform.sub = F,
  ...
)

Arguments

x

a numerical matrix features-by-samples

i

(optional) numerical vector giving the (row) position in x or character vector matching the (row) names in x. If missing or i = NULL, the entire x is considered for the computation of the score

na.rm

logical, whether to remove NA values from x before computation

transform.fun

function to transform the data. If provided, x is transformed (x = transform.fun(x, transform.args)) before the computation of the scores. See getDataTransformer for further details about built-in options

transform.args

list of parameters to the data transformation function

transform.sub

logical, whether to transform x after it is subset for i (used to speedup computation). Default is FALSE, meaning the transformation would be applied directly to x provided in input

...

further arguments to gsva

Value

A numerical value representing the computed score. A default NA value is returned if the score can't be computed, or if i values are not present in x.

Details

It is a wrapper to gsva function.

See also

gsva

Author

Alessandro Barberis