bioconductor-harmonizr

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name: bioconductor-harmonizr description: An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss. when_to_use: Use when: An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma; HarmonizR_Vignette. Not for: Requires R ≥ 4.2.0 and Bioconductor ≥ 3.16 user-invocable: false

HarmonizR

Workflows

Standard Workflow

Perform batch effect correction on a data frame containing missing values using ComBat or limma.

library(HarmonizR)

# 1. Prepare the input data frame and sample description data frame
df <- data.frame(matrix(rnorm(n = 3*6), ncol = 6))
colnames(df) <- c("A", "B", "C", "D", "E", "F")
rownames(df) <- c(  

batch   each  
des  data.frameID  colnamesdf sample   batch  batch


result  harmonizRdf des output_file   cores