ligandReceptorTest {CiteFuse} | R Documentation

## ligandReceptorTest

### Description

A function to perform ligand receptor analysis

### Usage

    ligandReceptorTest(
      sce,
      ligandReceptor_list,
      cluster,
      RNA_exprs_value = "minMax",
      use_alt_exp = TRUE,
      altExp_name = "ADT",
      altExp_exprs_value = "zi_minMax",
      num_permute = 1000,
      p_sig = 0.05
    )

### Arguments

`sce` | A singlecellexperiment object
`ligandReceptor_list` | A data.frame indicates the ligand receptor list
`cluster` | A vector indicates the cluster results
`RNA_exprs_value` | A character indicates which expression value for RNA in assayNames is used.
`use_alt_exp` | A logical vector indicates whether receptors expression will use alternative expression matrix to quantify.
`altExp_name` | A character indicates which expression matrix is used. by default is ADT .
`altExp_exprs_value` | A character indicates which expression value in assayNames is used.
`num_permute` | Number of permutation.
`p_sig` | A numeric indicates threshold of the pvalue significance

### Value

A SingleCellExperiment object with ligand receptor results

### Examples

    data(lr_pair_subset, package = "CiteFuse")
    data(sce_control_subset, package = "CiteFuse")

    sce_control_subset <- normaliseExprs(sce = sce_control_subset,
    altExp_name = "ADT",
    transform = "zi_minMax")

    sce_control_subset <- normaliseExprs(sce = sce_control_subset,
                                  altExp_name = "none",
                                  exprs_value = "logcounts",
                                  transform = "minMax")

    sce_control_subset <- ligandReceptorTest(sce = sce_control_subset,
                                      ligandReceptor_list = lr_pair_subset,
                                      cluster = sce_control_subset$SNF_W_louvain,
                                      RNA_exprs_value = "minMax",
                                      use_alt_exp = TRUE,
                                      altExp_name = "ADT",
                                      altExp_exprs_value = "zi_minMax",
                                      num_permute = 100)

[Package CiteFuse version 1.2.1 Index]