DaMiR.SVadjust: Remove variable effects from expression data

In DaMiRseq: Data Mining for RNA-seq data: normalization, feature selection and classification

Description

This function removes surrogate or other confounding variable effects from normalized expression data by the usage of removeBatchEffect function of limma package.

Usage

DaMiR.SVadjust(data, sv, n.sv)

Arguments

data	A SummarizedExpression object
sv	The matrix of surrogate variables identified by DaMiR.SV function
n.sv	The number of surrogate variables to be used to adjust the data

Value

A SummarizedExpression object containing a matrix of log-expression values with sv effects removed and the data frame of the variables.

Author(s)

Mattia Chiesa, Luca Piacentini

See Also

removeBatchEffect, DaMiR.SV

Examples

# use example data:
data(data_norm)
data(sv)
data_adjust <- DaMiR.SVadjust(data_norm, sv = sv, n.sv = 3)

DaMiRseq documentation built on Nov. 8, 2020, 5:53 p.m.