svacor: svacor

In plger/SEtools: SEtools: tools for working with SummarizedExperiment

svacor

Description

A wrapper around SVA-based correction, providing a corrected assay. If this is RNAseq data or similar, use a count assay assay with 'useVST=TRUE'; otherwise (e.g. proteomics) a log-normalized assay is recommended.

Usage

svacor(
  SE,
  form,
  form0 = ~1,
  assayName = NULL,
  regressOutNull = TRUE,
  useVST = TRUE,
  n.sv = NULL,
  ...
)

Arguments

SE	An object of class 'SummarizedExperiment'.
form	The formula of the differential expression model
form0	An optional formula for the null model
assayName	The name (or index) of the assay to use.
regressOutNull	Logical; whether to regress out the variables of 'form0'.
useVST	Logical; whether to use DESeq2's variance-stabilizing transformation; (for count data!)
n.sv	The number of surrogate variables (if omitted, sva will attempt to estimate it)
...	Any other argument passed to the sva command.

Value

Returns the 'SummarizedExperiment' with a 'corrrected' assay and the surrogate variables in 'colData'.

Examples

data("SE", package="SEtools")
SE <- svacor(SE, ~Condition)

plger/SEtools documentation built on Dec. 2, 2022, 3:58 p.m.