CiteFuse {CiteFuse} | R Documentation

## CiteFuse

### Description

A function to runSNF for CITE seq data

### Usage

    CiteFuse(
      sce,
      altExp_name = "ADT",
      W_list = NULL,
      gene_select = TRUE,
      dist_cal_RNA = "correlation",
      dist_cal_ADT = "propr",
      ADT_subset = NULL,
      K_knn = 20,
      t = 20,
      metadata_names = NULL,
      verbose = TRUE
    )

### Arguments

`sce` | a SingleCellExperiment
`altExp_name` | expression name of ADT matrix
`W_list` | affinity list, if it is NULL, the function will calculate it.
`gene_select` | whether highly variable genes will be selected for RNA-seq to calcualte simlarity matrix
`dist_cal_RNA` | similarity metrics used for RNA matrix
`dist_cal_ADT` | similarity metrics used for ADT matrix
`ADT_subset` | A vector indicates the subset that will be used.
`K_knn` | Number of nearest neighbours
`t` | Number of iterations for the diffusion process.
`metadata_names` | A vector indicates the names of metadata returned
`verbose` | whether print out the process

### Value

A SingleCellExperiment object with fused matrix results stored

### Examples

    data("sce_ctcl_subset", package = "CiteFuse")
    sce_ctcl_subset <- CiteFuse(sce_ctcl_subset)

[Package CiteFuse version 1.0.0 Index]