Combine several SingleCellExperiment objects from different batches/experiments

Combine several SingleCellExperiment objects from different batches/experiments. Extracted from the scMerge package.

sce_cbind(
  sce_list,
  method = "intersect",
  cut_off_batch = 0.01,
  cut_off_overall = 0.01,
  exprs = c("counts", "logcounts"),
  colData_names = NULL,
  batch_names = NULL
)

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
exprs	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

Value

A SingleCellExperiment object with the list of SCE objects combined.

Author

Yingxin Lin

Examples

library(scKirby)
data("example_sce")
batch_names<-unique(example_sce$batch)
sce_list<-list(example_sce[,example_sce$batch=='batch2'],
               example_sce[,example_sce$batch=='batch3'])
sce_combine<-sce_cbind(sce_list,batch_names=batch_names)
#> The assay named 'counts' will be used to determine the proportion of zeroes for each batch
#> Error in assay(y, exprs[i]): could not find function "assay"