PomaBatch: Batch Correction
In pcastellanoescuder/POMA: Tools for Omics Data Analysis

PomaBatch

R Documentation

Batch Correction

Description

PomaBatch performs batch correction on a SummarizedExperiment object given a batch factor variable.

Usage

PomaBatch(data, batch, mod = NULL)

Arguments

`data`	A `SummarizedExperiment` object.
`batch`	Character. The name of the column in `colData` that contains the batch information.
`mod`	Character vector. Indicates the names of `colData` columns to be included as covariates. Default is NULL (no covariates).

Value

A SummarizedExperiment object with batch-corrected data.

Author(s)

Pol Castellano-Escuder

References

Leek JT, Johnson WE, Parker HS, Fertig EJ, Jaffe AE, Zhang Y, Storey JD, Torres LC (2023). sva: Surrogate Variable Analysis. doi:10.18129/B9.bioc.sva https://doi.org/10.18129/B9.bioc.sva

Examples

# Output is a batch corrected SummarizedExperiment object
data <- POMA::st000284 # Example SummarizedExperiment object included in POMA

data %>%
  PomaBatch(batch = "gender")

pcastellanoescuder/POMA documentation built on Oct. 13, 2024, 8:46 p.m.