Merge gene expression data from multiple studies.

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

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.