bapred (version 1.1)

corba: Mean correlation before and after batch effect adjustment

Description

For each variable Pearson's correlation of the values before and after batch effect adjustment is calculated. Then the mean is taken over all these correlations.

Usage

corba(xba, x)

Arguments

xba

matrix. The covariate matrix after batch effect adjustment. observations in rows, variables in columns.

x

matrix. The covariate matrix before batch effect adjustment. observations in rows, variables in columns.

Value

Value of the metric

References

Lazar, C., Meganck, S., Taminau, J., Steenhoff, D., Coletta, A., Molter,C., Weiss-Sol<U+00ED>s, D. Y., Duque, R., Bersini, H., Now<U+00E9>, A. (2012). Batch effect removal methods for microarray gene expression data integration: a survey. Briefings in Bioinformatics 14(4):469-490, <10.1093/bib/bbs037>.

Examples

# NOT RUN {
data(autism)

params <- ba(x=X, y=y, batch=batch, method = "combat")
Xadj <- params$xadj

corba(xba=Xadj, x=X)
# }