sce_cbind {scMerge} | R Documentation

## Combind several `SingleCellExperiment` objects from different batches/experiments

### Description

Combind several `SingleCellExperiment` objects from different batches/experiments.

### Usage

    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 zeores.
`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(s)

Yingxin Lin

### Examples

    data('example_sce', package = 'scMerge')
    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)

[Package scMerge version 1.4.0 Index]