topHits {MetaNeighbor} | R Documentation |
Identifies reciprocal top hits and high scoring cell type pairs
topHits(cell_NV, dat, i = 1, study_id, cell_type, threshold = 0.95)
cell_NV |
matrix of celltype-to-celltype AUROC scores
(output from |
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] |
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
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