SpaCo: SpaCo

In SPACO: Spatial Component Analysis for Spatial Sequencing Data

SpaCo

Description

SpaCo

Usage

SpaCo(
  SpaCoObject,
  PC_criterion = "percent",
  PC_value = 0.95,
  set_nspacs = NULL,
  nSim = 1000,
  nSpacQuantile = 0.05,
  reducedSpots = FALSE,
  nReduce = 1000
)

Arguments

SpaCoObject	Object of class SpaCoObject as generated from [SpaCoObject] on which to perform SCA.
PC_criterion	criterion on which to select number of principal components for initial covariance matrix reconstruction; either "number" to select a number of PCs or "percent" to select number of PCs to explain specified amount of data variance
PC_value	Value to specify number of PCs or desired level of explained variance, see "PC_criterion"
set_nspacs	Boolean if number of relevant spacs is to be computed. Increases run time significantly
nSim	Number of simulations for computation of spac number
nSpacQuantile	Quantile to use as cutoff for spac number
reducedSpots	Should algorithm be run on a subset of spots? Default = FALSE
nReduce	Number of spots to sample to run algorithm on subset if reducedSpots==TRUE. Ignored if reducedSpots==FALSE

Value

Returns a SpaCoObject filled with the result of the spatial component analysis.

SPACO documentation built on March 31, 2026, 5:07 p.m.