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(input_sm, out_chs, ...)

## S4 method for signature 'matrix,vector'
adaptSpillmat(input_sm, out_chs,
  isotope_list = CATALYST::isotope_list)

Arguments

input_sm

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. Ir191Di or Ir191, will be interpreted as masses with associated metals.

...

optional arguments.

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.

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 Lucia Crowell crowellh@student.ethz.ch and Vito RT Zanotelli vito.zanotelli@uzh.ch

Examples

# get single-stained control samples
data(ss_exp)
# specify mass channels stained for
bc_ms <- c(139, 141:156, 158:176)
# debarcode
re <- assignPrelim(x = ss_exp, y = bc_ms)
re <- estCutoffs(x = re)
re <- applyCutoffs(x = re)
# estimate spillover matrix and adapt it
sm <- computeSpillmat(x = re)
chs <- flowCore::colnames(ss_exp)
adaptSpillmat(sm, chs)


[Package CATALYST version 1.4.2 Index]