Hierarchical RUV

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.

assay

An assay name to measure the missingness of the signals.

k

Parameter k for RUV-III.

rep

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

newAssay

A name of the new assay for cleaned (preprocessed) data.

balanced

A type of hierarchical approach, "concatenate" or "balanced". Default is "concatenate" approach.

negCtl

A vector of row IDs for selection of stable matbolites to be used as negative control in RUV.

hOrder

A vector of batch names from names of list dat_list.

Value

A normalised data as SummarizedExperiment object.