benchmark {granulator}R Documentation

Regress estimated cell type proportions against the ground truth

Description

regress computes regression between estimated cell type proportions and the measured cell type proportions (ground truth).

Usage

benchmark(deconvoluted, ground_truth)

Arguments

deconvoluted

Output object of the function deconvolute.

ground_truth

A matrix containing measured cell type proportions in percentages. Samples names are inlcuded in rownames.

Value

Returns a list containing thres elements:

Author(s)

Vincent Kuettel, Sabina Pfister

Examples

# load demo PBMCS data
load_ABIS()

# deconvolute
decon <- deconvolute(m = bulkRNAseq_ABIS, 
sigMatrix = sigMatrix_ABIS_S0)

# bechmark
bench <- benchmark(deconvoluted = decon, 
ground_truth = groundTruth_ABIS)


[Package granulator version 1.2.0 Index]