ewaff.sva: Generate surrogate variables using the ewaff.sites syntax

In perishky/ewaff: Efficient and Flexible EWAS

Generate surrogate variables using the ewaff.sites syntax

Description

Provide a function to manually compute surrogate variables, using the same syntax for submission of a ewaff.sites call

Usage

ewaff.sva(
  formula,
  variable.of.interest,
  methylation,
  data,
  family = gaussian,
  n.sv = 10,
  most.variable = NULL,
  random.subset = 0.05,
  algorithm = "sva",
  ...
)

Arguments

formula	An object of class formula: a symbolic description of the model to be fitted. DNA methylation is referred to by the variable name 'methylation'.
variable.of.interest	Name of variable in the GLM model formula for which to save summary statistics.
methylation	DNA methylation matrix, one row per CpG site, one column per sample.
data	Data frame providing variables referenced in model formula.
family	(Default: gaussian).
n.sv	Number of surrogate variables to compute (Default: 10).
most.variable	Generate surrogate variables from the given most variable CpG sites rather than the whole matrix (Default: NULL).
random.subset	Generate surrogate variables from the given percentage of randomly selected CpG sites rather than the whole matrix (Default: 0.05, i.e. 5 percent).
algorithm	Algorithm to use, either "sva" or "smartsva" (Default: "sva").

Details

Note: surrogate variables are computed using sva

Value

Matrix containing surrogate variables computed

perishky/ewaff documentation built on Jan. 31, 2024, 11:29 p.m.