batchNormalization: Batch Normalization

In jordirofes/OmniOmics: Analysis of metabolomics (LC-MS) and transcriptomics (Microarray) data

Batch Normalization

Description

Makes the batch normalization for injection order (Metabolomics) using the pmp package and covariates (Transcriptomics) using the pvca package.

Usage

batchNormalization(
  features,
  method,
  injectionorder,
  batchnum,
  groups,
  qcname,
  covariate,
  covariate2 = NULL
)

Arguments

features	An ExpressionSet or SummarizedExperiment object
method	A string for the normalization method: qcnorm for injection order and batch normalization and covnorm for covariate normalization
injectionorder	A string or numerical indicating the variable in the phenodata with the injection order or a vector with the injection order.
batchnum	A string or numerical indicating the variable in the phenodata with the batch number
groups	A string or numerical indicating the variable in the phenodata with the grouping variable (QC/SAMPLE/...)
qcname	A string with the name of the QC samples in the groups variable
covariate	A string or numerical indicating the variable in the phenodata with the first covariate to normalize
covariate2	An optional string or numerical indicating the variable in the phenodata with the second covariate to normalize

Value

Returns a covariate/batch corrected ExpressionSet or SummarizedExperiment

Author(s)

Jordi Rofes Herrera

jordirofes/OmniOmics documentation built on Nov. 22, 2022, 5:46 a.m.