adaptSpillmat {CATALYST} | R Documentation

## 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 helena.crowell@uzh.ch & 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))

[Package CATALYST version 1.14.1 Index]