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 1.13.0 Index]