bapred (version 0.3)

standardizeaddon: Addon batch effect adjustment for standardization

Description

Performs addon batch effect adjustment for standardization: 1) takes the output of standardize applied to a training data set together with new batch data; 2) checks whether the training data was also adjusted using standardization and whether the same number of variables is present in training and new data; 3) performs standardization on the new batch data.

Usage

standardizeaddon(params, x, batch)

Arguments

params

object of class standardize.

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.

Value

• The adjusted covariate matrix of the test data.

References

Hornung, R., Boulesteix, A.-L., Causeur, D. (2016) Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment. BMC Bioinformatics 17:27.

Examples

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 <- standardize(x=Xtrain, batch=batchtrain)

Xtestaddon <- standardizeaddon(params=params, x=Xtest, batch=batchtest)