scale_batch_effects: Obtain the scale batch effects from the output by 'BUSgibbs'

In XiangyuLuo/BUScorrect: Batch Effects Correction with Unknown Subtypes

Description

Call the function to obtain the scale batch effects from the output by BUSgibbs.

Usage

scale_batch_effects(BUSfits)

Arguments

BUSfits

The BUSfits object output by the function BUSgibbs.

Value

est_scale_batch_effects

The estimated scale batch effects, a matrix where rows are genes and columns are batches.

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)
est_scale_batch_effects <- scale_batch_effects(BUSfits)

XiangyuLuo/BUScorrect documentation built on June 14, 2019, 3:31 p.m.