location_batch_effects: Obtain the location batch effects from the output by BUSgibbs

Description Usage Arguments Value Author(s) References Examples

View source: R/BUS_Rfunctions.R

Description

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

Usage

1

Arguments

BUSfits

The BUSfits object output by the function BUSgibbs.

Value

est_location_batch_effects

The estimated location batch effects, a matrix whose rows represent genes and columns correspond to batches.

Author(s)

Xiangyu Luo

References

Xiangyu Luo, Yingying Wei. Batch Effects Correction with Unknown Subtypes. Journal of the American Statistical Association. Accepted.

Examples

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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_location_batch_effects <- location_batch_effects(BUSfits)

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