adaptSpillmat: Adapt spillover matrix

In HelenaLC/CATALYST: Cytometry dATa anALYSis Tools

Adapt spillover matrix

Description

This helper function adapts the columns of a provided spillover matrix such that it is compatible with data having the column names provided.

Usage

adaptSpillmat(
  x,
  out_chs,
  isotope_list = CATALYST::isotope_list,
  verbose = TRUE
)

Arguments

x	a previously calculated spillover matrix.
out_chs	the column names that the prepared output spillover matrix should have. Numeric names as well as names of the form MetalMass(Di), e.g. Ir191, Ir191Di or Ir191(Di), will be interpreted as masses with associated metals.
isotope_list	named list. Used to validate the input spillover matrix. Names should be metals; list elements numeric vectors of their isotopes. See isotope_list for the list of isotopes used by default.
verbose	logical. Should warnings about possibly inaccurate spillover estimates be printed to the console?

Details

The rules how the spillover matrix is adapted are explained in compCytof.

Value

An adapted spillover matrix with column and row names according to out_chs.

Author(s)

Helena L Crowell [e-mail] & Vito RT Zanotelli

Examples

# estimate spillover matrix from 
# single-stained control samples
data(ss_exp)
sce <- prepData(ss_exp)
bc_ms <- c(139, 141:156, 158:176)
sce <- assignPrelim(sce, bc_ms, verbose = FALSE)
sce <- applyCutoffs(estCutoffs(sce))
sce <- computeSpillmat(sce)

library(SingleCellExperiment)
sm1 <- metadata(sce)$spillover_matrix
sm2 <- adaptSpillmat(sm1, rownames(sce), verbose = FALSE)
all(dim(sm2) == ncol(sm1))

HelenaLC/CATALYST documentation built on Nov. 30, 2024, 4:04 a.m.