aggregate_classic_patch: Calculates patch detection neightbourhood statistics

In BodenmillerGroup/neighbouRhood: neighbouRhood analysis in R

Description

Calculates: What fraction of cells of type A have at least a given number of neighbours of type B?

Usage

aggregate_classic_patch(dat_nb, patch_size)

Arguments

dat_nb	a neightbourhood table with the labels applied with 'apply_labels'
patch_size	minimum number of neighbours to be considered a patch

Details

This was first proposed in Schulz D, Zanotelli VRT, Fischer JR, Schapiro D, Engler S, Lun XK, Jackson HW, Bodenmiller B. Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry. Cell Syst. 2018 Jan 24;6(1):25-36.e5. doi: 10.1016/j.cels.2017.12.001

Value

a statistics with columns group, Firstlabel, Secondlabel, ct

BodenmillerGroup/neighbouRhood documentation built on Sept. 9, 2021, 4:49 a.m.