FilterCODEX: Removes points from CODEX matrix that are not cells as...

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

Removes points from CODEX matrix that are not cells as determined by the gating strategy on the blank channels from the CODEX paper

Description

Removes points from CODEX matrix that are not cells as determined by the gating strategy on the blank channels from the CODEX paper

Usage

FilterCODEX(
  stvea_object,
  size_lim = NULL,
  blank_upper = NULL,
  blank_lower = NULL
)

Arguments

stvea_object	STvEA.data class with CODEX data
size_lim	lower and upper limits on size of each cell. If blank, set to 0.025 and 0.99 quantiles
blank_upper	a vector with an upper bound expression cutoff for each blank channel. If NULL, blank upper bounds are set as the 0.995 quantile for each blank
blank_lower	a vector with a lower bound expression cutoff for each blank channel. If NULL, blank lower bounds are set as the 0.002 quantile for each blank

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