mergeSEs: mergeSEs
In SEtools: SEtools: tools for working with SummarizedExperiment

Description Usage Arguments Value Examples

View source: R/mergeSEs.R

Merges a list of SummarizedExperiment-class, either by row.names or through specified rowData fields. In cases of many-to-many (or one-to-many) mappings, 'aggFun' determines whether the records are aggregated by linking ID (if an aggregation method is given) or all combinations are returned (if 'aggFun=NULL' - default).

mergeSEs(
  ll,
  use.assays = NULL,
  do.scale = TRUE,
  commonOnly = TRUE,
  colColumns = NULL,
  mergeBy = NULL,
  aggFun = NULL,
  addDatasetPrefix = TRUE,
  defValues = list(),
  keepRowData = TRUE,
  BPPARAM = SerialParam()
)

`ll`	A (named) list of `SummarizedExperiment-class`
`use.assays`	Names (or indexes) of the assays to use. By default, all common assays are used.
`do.scale`	A logical vector indicating (globally or for each assay) whether to perform row unit-variance scaling on each dataset before merging (default TRUE).
`commonOnly`	Logical; whether to restrict to rows present in all datasets (default TRUE).
`colColumns`	A character vector specifying 'colData' columns to include (if available in at least one of the datasets). If NULL, everything is kept.
`mergeBy`	The 'rowData' column to merge with. If NULL, row.names are used.
`aggFun`	The aggregation function to use when multiple rows have the same 'mergeBy' value. If merging multiple assays, a different function per assay can be passed as a named list (see `aggSE`). If NULL (default), entries will be reused to have each combination.
`addDatasetPrefix`	Logical; whether the name of the dataset should be appended to the sample names (default TRUE).
`defValues`	An optional named list of default 'colData' values when some columns are missing from some SEs.
`keepRowData`	Logical, whether to keep the rowData (default TRUE).
`BPPARAM`	For multithreading the aggregation step.