filterPixels: Filter pixels based on their assigned masses

In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis

Filter pixels based on their assigned masses

Description

Helper function for estimating the spillover matrix. After assigning each pixel to a spotted mass, this function will filter incorrectly assigned pixels and remove small pixel sets.

Usage

filterPixels(
  object,
  bc_id = "bc_id",
  spot_mass = "sample_mass",
  minevents = 40,
  correct_pixels = TRUE
)

Arguments

object	a SingleCellExperiment object containing pixel intensities per channel. Individual pixels are stored as columns and channels are stored as rows.
bc_id	character string indicating which colData(object) entry stores the estimated mass
spot_mass	character string indicating which colData(object) entry stores the true isotope mass of the spotted metal.
minevents	single numeric indicating the threshold under which pixel sets are excluded from spillover estimation.
correct_pixels	logical indicating if incorrectly assigned pixels should be excluded from spillover estimation.

Value

returns a SingleCellExperiment object in which colData(object)$bc_id has been adjusted based on the filter criteria.

Author(s)

Vito Zanotelli, adapted by Nils Eling ([e-mail])

Examples

path <- system.file("extdata/spillover", package = "imcRtools")
sce <- readSCEfromTXT(path)
assay(sce, "exprs") <- asinh(counts(sce)/5)

# Pre-process via CATALYST
library(CATALYST)

bc_key <- as.numeric(unique(sce$sample_mass))
sce <- assignPrelim(sce, bc_key = bc_key)
sce <- estCutoffs(sce)
sce <- applyCutoffs(sce)

sce <- filterPixels(sce)

table(sce$sample_mass, sce$bc_id)

BodenmillerGroup/imcRtools documentation built on July 1, 2024, 5:15 p.m.