Hierarchical RUV

hierarchy(
dat_list,
assay,
k = 5,
rep,
newAssay = NULL,
balanced = FALSE,
negCtl = NULL,
hOrder = NULL
)

## Arguments

dat_list A list of SummarizedExperiment data where each object represents a batch. An assay name to measure the missingness of the signals. Parameter k for RUV-III. A name of the variable in the colData of each SummarizedExperiment data in the dat_list. This variable in colData should be a logical vector of whic samples are a intra-batch replicate A name of the new assay for cleaned (preprocessed) data. A type of hierarchical approach, "concatenate" or "balanced". Default is "concatenate" approach. A vector of row IDs for selection of stable matbolites to be used as negative control in RUV. A vector of batch names from names of list dat_list.

## Value

A normalised data as SummarizedExperiment object.