adjusted_values {BUScorrect}R Documentation

Obtain adjusted expression values from the output by BUSgibbs

Description

Call the function to obtain the corrected expression values with batch effects removed from the original input data.

Usage

adjusted_values(BUSfits, original_data)

Arguments

BUSfits

The BUSfits object output by the function BUSgibbs.

original_data

The original gene expression data list with length equal to the batch number. Each of its element is a gene expression matrix for a specific batch, in which each row corresponds to a gene and each column corresponds to a sample.

Value

adjusted_data

An R list with length equal to the batch number. Each of its element is a corrected gene expression matrix for a specific batch, in which each row corresponds to a gene and each column corresponds to a sample.

Author(s)

Xiangyu Luo

References

Xiangyu Luo, Yingying Wei. Batch Effects Correction with Unknown Subtypes. Journal of the American Statistical Association. Accepted.

Examples

rm(list = ls(all = TRUE))  
set.seed(123)
#a toy example, there are 6 samples and 20 genes in each batch
example_Data <- list()

#batch 1
example_Data[[1]] <- rbind(matrix(c(1,1,5,5,10,10,
						3,3,7,7,12,12), ncol=6, byrow=TRUE), matrix(c(1,2),nrow=18, ncol=6))

#batch 2
batch2_effect <- c(2,2,2,1,1)
example_Data[[2]] <- rbind(matrix(c(1,1,5,5,10,10,
						3,3,7,7,12,12), ncol=6, byrow=TRUE), matrix(c(1,2),nrow=18, ncol=6)) + batch2_effect

#batch 3
batch3_effect <- c(3,2,1,1,2)
example_Data[[3]] <- rbind(matrix(c(1,1,5,5,10,10,
						3,3,7,7,12,12), ncol=6, byrow=TRUE), matrix(c(1,2),nrow=18, ncol=6)) + batch3_effect

set.seed(123)
BUSfits <- BUSgibbs(example_Data, n.subtypes = 3, n.iterations = 100, showIteration = FALSE)						
adjusted_data <- adjusted_values(BUSfits, example_Data)


[Package BUScorrect version 1.12.0 Index]