topHits {MetaNeighbor} | R Documentation

## Find reciprocal top hits

### Description

Identifies reciprocal top hits and high scoring cell type pairs. This function only look for the overall top hit for each cell type. We strongly recommend using topHitsByStudy instead, which looks for top hits in each target study, providing a more comprehensive view of replicability.

### 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

### See Also

`topHitsByStudy`

### 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 1.14.0 Index]