preprocessing {CiteFuse} | R Documentation

## A function to preprocess the list of expression matrix

### Description

This function will keep the samples that are common across the list of expression matrix, and filter the features that are all zeros across samples, and finally construct a `SingleCellExperiment` object

### Usage

    preprocessing(
      exprsMat = NULL,
      return_sce = TRUE,
      assay_matrix = 1,
      filter_features = TRUE,
      rowData = NULL,
      colData = NULL
    )

### Arguments

`exprsMat` | A list or a matrix indicates the expression matrices of the testing datasets (each matrix must be `matrix` or `dgCMatrix` class)
`return_sce` | A logical input indicates whether a `SingleCellExperiment` object will be return
`assay_matrix` | A integer indicates which list will be used as 'assay' input of 'SingleCellExperiment'
`filter_features` | A logical input indicates whether the features with all zeros will be removed
`rowData` | A DataFrame indicates the rowData to be stored in the sce object
`colData` | A DataFrame indicates the colData to be stored in the sce object

### Value

either a SingleCellExperiment object or a preprocessed expression matrix

### Examples

    data(CITEseq_example, package = "CiteFuse")
    sce_citeseq <- preprocessing(CITEseq_example)

[Package CiteFuse version 1.2.1 Index]