adjusted_values {BUScorrect} | R Documentation |
Call the function to obtain the corrected expression values with batch effects removed from the original input data.
adjusted_values(BUSfits, original_data)
BUSfits |
The BUSfits object output by the function |
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. |
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. |
Xiangyu Luo
Xiangyu Luo, Yingying Wei. Batch Effects Correction with Unknown Subtypes. Journal of the American Statistical Association. Accepted.
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)