View source: R/combatbaaddon.R
combatbaaddon | R Documentation |
Performs addon batch effect adjustment using ComBat. Takes the output of performing combatba
on a training data set and new batch data and correspondingly adjusts the test data to better match the adjusted training data according to the ComBat model
combatbaaddon(params, x, batch)
params |
object of class |
x |
matrix. The covariate matrix of the new data. Observations in rows, variables in columns. |
batch |
factor. Batch variable of the new data. Currently has to have levels: '1', '2', '3' and so on. |
The adjusted covariate matrix of the test data.
The original ComBat-code is used in combatbaaddon
:
http://www.bu.edu/jlab/wp-assets/ComBat/Download.html (Access date: 2015/06/19)
Roman Hornung
Johnson, W. E., Rabinovic, A., Li, C. (2007). Adjusting batch effects in microarray expression data using empirical bayes methods. Biostatistics 8:118-127, <doi: 10.1093/biostatistics/kxj037>.
Luo, J., Schumacher, M., Scherer, A., Sanoudou, D., Megherbi, D., Davison, T., Shi, T., Tong, W., Shi, L., Hong, H., Zhao, C., Elloumi, F., Shi, W., Thomas, R., Lin, S., Tillinghast, G., Liu, G., Zhou, Y., Herman, D., Li, Y., Deng, Y., Fang, H., Bushel, P., Woods, M., Zhang, J. (2010). A comparison of batch effect removal methods for enhancement of prediction performance using maqc-ii microarray gene expression data. The Pharmacogenomics Journal 10:278-291, <doi: 10.1038/tpj.2010.57>.
data(autism) trainind <- which(batch %in% c(1,2)) Xtrain <- X[trainind,] ytrain <- y[trainind] batchtrain <- factor(as.numeric(batch[trainind]), levels=c(1,2)) testind <- which(batch %in% c(3,4)) Xtest <- X[testind,] ytest <- y[testind] batchtest <- as.numeric(batch[testind]) batchtest[batchtest==3] <- 1 batchtest[batchtest==4] <- 2 batchtest <- factor(batchtest, levels=c(1,2)) params <- combatba(x=Xtrain, batch=batchtrain) Xtestaddon <- combatbaaddon(params, x=Xtest, batch=batchtest)
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