Construct a SingleCellExperiment object with specified covariates.

Usage

constructSCE(
  data_obj,
  cellcov_df = NULL,
  featcov_df = NULL,
  cellcov_names,
  sampid_vec = NULL,
  overlap_features = NULL,
  assay_name = "RNA",
  slot_name = "counts",
  sce_name = slot_name,
  indiv_colname = "indiv",
  celltype_colname = "cell_type",
  factor_colnames = NULL,
  cellcov_renames = cellcov_names
)

Arguments

data_obj: a Seurat, SingleCellExperiment, or expression matrix (gene-by-cell) used to construct the new SingleCellExperiment object.
cellcov_df: a dataframe containing covariates for all cells. Row names must have cell names that match data_obj. Only used when data_obj is a matrix object.
featcov_df: a dataframe containing covariates for all features (ie genes). Row names must have feature names that match data_obj. Only used when data_obj is a matrix object.
cellcov_names: a string vector of all columns to extract from cell covariates.
sampid_vec: an optional string vector of sample ids (individuals). Default is NULL. If provided, it must match sample ids found in data_obj.
overlap_features: an optional string vector for features to filter data_obj. Default is NULL. If provided, all features must be present in the data_obj.
assay_name: a string scalar of name of the Seurat object slot of interest. Only used if data_obj is a Seurat object.
slot_name: a string scalar for the type of assay data (either 'logcounts' or 'counts'). Default is 'counts'. Only used if data_obj is a Seurat or SingleCellExperiment object.
sce_name: a string scalar for the type of assay data for output SingleCellExperiment.
indiv_colname: a string scalar for the sample id colname. Must be present in cellcov_df or data_obj. Default is 'indiv'.
celltype_colname: a string scalar for the cell type colname. Must be present in cellcov_df or data_obj. Default is 'cell_type'.
factor_colnames: an optional string vector or scalar for the columns to coerce into factor variables. Default is NULL. If provided, it must be present in cellcov_df or data_obj.
cellcov_renames: an optional string vector to rename the cell covariates. Must be same length as cellcov_names. Default is same as cellcov_names.

Value

a SingleCellExperiment object

Examples

NULL
#> NULL