AdjScoreClustersCITE: Use the Adjacency Score to evaluate colocaliztion of all...

View source: R/feature_scores.R

AdjScoreClustersCITER Documentation

Use the Adjacency Score to evaluate colocaliztion of all pairs of CITE-seq clusters mapped to the CODEX spatial positions

Description

Use the Adjacency Score to evaluate colocaliztion of all pairs of CITE-seq clusters mapped to the CODEX spatial positions

Usage

AdjScoreClustersCITE(
  stvea_object,
  k,
  c = 0,
  num_cores = 1,
  num_perms = 1000,
  perm_estimate = T
)

Arguments

stvea_object

STvEA.data class object containing CITE-seq cluster assignments, CODEX spatial coordinates, and transfer matrix from GetTransferMatrix

k

number of nearest neighbors to create graph from CODEX spatial information

c

constant used to determine width of diffusion, must be 0 <= c

num_cores

integer specifying the number of cores to be used in the computation. By default only one core is used. On Windows, this must be set to 1.

num_perms

number of permutations used to build the null distribution for each feature. By default is set to 1000.

perm_estimate

boolean indicating whether Gaussian distribution parameters should be determined from num_perms permutations to estimate the p-value. By default is set to TRUE.


CamaraLab/STvEA documentation built on March 27, 2024, 8:58 a.m.