topHits {MetaNeighbor} | R Documentation

## Find reciprocal top hits

### Description

Identifies reciprocal top hits and high scoring cell type pairs

### Usage

    topHits(cell_NV, dat, i = 1, study_id, cell_type, threshold = 0.95)

### Arguments

`cell_NV` | matrix of celltype-to-celltype AUROC scores (output from `MetaNeighborUS`)
`dat` | a SummarizedExperiment object containing gene-by-sample expression matrix.
`i` | default value 1; non-zero index value of assay containing the matrix data
`study_id` | a vector that lists the Study (dataset) ID for each sample
`cell_type` | a vector that lists the cell type of each sample
`threshold` | default value 0.95. Must be between [0,1]

### Value

Function returns a dataframe with cell types that are either reciprocal best matches, and/or those with AUROC values greater than or equal to threshold value

### Examples

    data(mn_data)
    var_genes = variableGenes(dat = mn_data, exp_labels = mn_data$study_id)
    celltype_NV = MetaNeighborUS(var_genes = var_genes,
                                 dat = mn_data,
                                 study_id = mn_data$study_id,
                                 cell_type = mn_data$cell_type)
    top_hits = topHits(cell_NV = celltype_NV,
                       dat = mn_data,
                       study_id = mn_data$study_id,
                       cell_type = mn_data$cell_type,
                       threshold = 0.9)
    top_hits

[Package MetaNeighbor version 1.2.1 Index]