PomaBatch: Batch Correction

In pcastellanoescuder/POMA: Tools for Omics Data Analysis

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

data("st000284")

st000284 %>%
PomaImpute(method = "knn") %>% 
PomaBatch(batch = "gender")

pcastellanoescuder/POMA documentation built on March 15, 2024, 10:08 p.m.