CleanCODEX: Removes noise from CODEX data by fitting a Gaussian mixture...

In CamaraLab/STvEA: Spatially-resolved Transcriptomics via Epitope Anchoring

Removes noise from CODEX data by fitting a Gaussian mixture and computing each expression measurement as the cumulative distribution of the Gaussian with the higher mean.

Description

Removes noise from CODEX data by fitting a Gaussian mixture and computing each expression measurement as the cumulative distribution of the Gaussian with the higher mean.

Usage

CleanCODEX(
  stvea_object,
  model = "gaussian",
  num_cores = 1,
  maxit = 500,
  factr = 1e-09,
  optim_inits = NULL,
  normalize = FALSE
)

Arguments

stvea_object	STvEA.data class with CODEX data after FilterCODEX
model	"nb" (Negative Binomial) or "gaussian" model to fit or "arcsinh" for standard arcsinh transform (wrapper of flowCore method)
num_cores	number of cores to use for parallelized fits
maxit	maximum number of iterations for optim function - only used if model is "nb"
factr	accuracy of optim function - only used if model is "nb"
optim_inits	a matrix of (proteins x params) with initialization parameters for each protein to input to the optim function. If NULL, starts at two default parameter sets and picks the better one - only used if model is "nb"
normalize	divide cleaned CODEX expression by total expression per cell - only used if model is "nb"

CamaraLab/STvEA documentation built on April 2, 2024, 6:07 a.m.