baseline_expression_values: Obtain the baseline expression values from the output by...

In XiangyuLuo/BUScorrect: Batch Effects Correction with Unknown Subtypes

Description

Call the function to obtain the baseline expression values for subtype 1 from the output by BUSgibbs.

Usage

baseline_expression_values(BUSfits)

Arguments

BUSfits

The BUSfits object output by the function BUSgibbs.

Value

est_baseline_expression_values

The estimated baseline expression values for subtype 1, a vector with length equal to the gene number.

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_baseline_expression_values <- baseline_expression_values(BUSfits)

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