Merge gene expression data from multiple studies. — mergeStudyData • metapredict

Merge gene expression data from multiple studies, keeping only genes measured in each dataset, then optionally perform cross-study normalization using sva::ComBat().

Usage

mergeStudyData(
  ematList,
  sampleMetadata,
  batchColname = "study",
  covariateName = NA,
  batchCorrection = TRUE,
  parPrior = TRUE
)

Arguments

ematList: list of expression matrices.
sampleMetadata: data.frame for sample metadata.
batchColname: column in sampleMetadata containing batch information for ComBat.
covariateName: column in sampleMetadata containing additional covariates for ComBat besides batch.
batchCorrection: TRUE indicates cross-study normalization will be performed, FALSE indicates datasets will be merged without performing normalization.
parPrior: passed to ComBat's par.prior argument.

Value

A matrix of expression for genes by samples.