location_batch_effects {BUScorrect} | R Documentation |
Call the function to obtain the location batch effects from the output by BUSgibbs
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location_batch_effects(BUSfits)
BUSfits |
The BUSfits object output by the function |
est_location_batch_effects |
The estimated location batch effects, a matrix whose rows represent genes and columns correspond to batches. |
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_location_batch_effects <- location_batch_effects(BUSfits)