BIC_BUS: Obtain BIC form the output by BUSgibbs

In BUScorrect: Batch Effects Correction with Unknown Subtypes

Description

The BIC value can be used to determine the subtype number if it is unknown to the users.

Usage

BIC_BUS(BUSfits)

Arguments

BUSfits

The BUSfits object from the function BUSgibbs.

Value

BIC_val

The BIC value for the BUS model with the subtype number being n.subtypes, the input subtype number for the BUSgibbs function that generates the BUSfits object.

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)
BIC_val <- BIC_BUS(BUSfits)

BUScorrect documentation built on Nov. 8, 2020, 8:06 p.m.