prepare_sce_for_merge: Helper function to prepare an SCE object for merging

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

Helper function to prepare an SCE object for merging

Description

Helper function to prepare an SCE object for merging

Usage

prepare_sce_for_merge(
  sce,
  sce_name,
  batch_column,
  cell_id_column,
  shared_features,
  retain_coldata_cols,
  preserve_rowdata_cols,
  is_altexp = FALSE
)

Arguments

sce	The SCE object to be prepared
sce_name	The name of the SCE object
batch_column	The name of the batch column which will be added to the colData slot
cell_id_column	The name of the cell_id column which will be added to the colData slot
shared_features	A vector of features (genes) that all SCEs to be merged have in common
retain_coldata_cols	A vector of columns to retain in the colData slot. If columns are missing from the data, they will be filled with 'NA' values. The exceptions to this are 'barcode_column' and 'batch_column' which will be populated with respective information.
preserve_rowdata_cols	A vector of rowData columns which should not be renamed
is_altexp	Boolean if we are preparing an altExp or not. Default is 'FALSE'. If FALSE, the SCE colnames will not be modified.

Value

An updated SCE that is prepared for merging

AlexsLemonade/scpcaTools documentation built on July 12, 2024, 8:34 a.m.