topHits: Find reciprocal top hits

In mm-shah/MetaNeighbor: Single cell replicability analysis

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

mm-shah/MetaNeighbor documentation built on May 20, 2019, 1:29 p.m.