Merge multiple SingleCellExperiment objects

Merge several SingleCellExperiment (SCE) objects from different batches/experiments. Extracted from the scMerge package.

merge_sce(
  sce_list,
  method = "intersect",
  cut_off_batch = 0.01,
  cut_off_overall = 0.01,
  use_assays = NULL,
  colData_names = NULL,
  batch_names = NULL,
  verbose = TRUE
)

Source

scMerge.

Arguments

sce_list: A list contains the SingleCellExperiment Object from each batch.
method: A string indicates the method of combining the gene expression matrix, either union or intersect. Default to intersect. union only supports matrix class.
cut_off_batch: A numeric vector indicating the cut-off for the proportion of a gene is expressed within each batch.
cut_off_overall: A numeric vector indicating the cut-off for the proportion of a gene is expressed overall data.
use_assays: A string vector indicating the expression matrices to be combined. The first assay named will be used to determine the proportion of zeros.
colData_names: A string vector indicating the colData that are combined.
batch_names: A string vector indicating the batch names for the output SCE object.
verbose: Print messages.

Value

A SingleCellExperiment object with the list of SCE objects combined.

Author

Yingxin Lin (modified by Brian Schilder)

Examples

ctd <- ewceData::ctd()
#> see ?ewceData and browseVignettes('ewceData') for documentation
#> loading from cache
sce_list <- EWCE::ctd_to_sce(object = ctd)
#> + CTD ==> SingleCellExperiment
#> Converting level:  level_1
#> Returning all possible matrix names.
#> Converting level:  level_2
#> Returning all possible matrix names.
sce_combine <- merge_sce(sce_list = sce_list)
#> The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.