Subtypes: Obtain the subtype indicators from the output by 'BUSgibbs'
In BUScorrect: Batch Effects Correction with Unknown Subtypes

Description Usage Arguments Value Author(s) References Examples

Call the function to obtain the subtype indicators from the output by BUSgibbs.

1	Subtypes(BUSfits)

BUSfits

The BUSfits object output by the function BUSgibbs.

est_subtypes

The estimated subtypes, an R list with length equal to the batch number. The bth element is the estimated subtype indicator vector for samples in batch b.

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)
est_subtypes <- Subtypes(BUSfits)