adaptSpillmat {CATALYST} | R Documentation |
This helper function adapts the columns of a provided spillover matrix such that it is compatible with data having the column names provided.
adaptSpillmat(input_sm, out_chs, ...) ## S4 method for signature 'matrix,vector' adaptSpillmat(input_sm, out_chs, isotope_list = CATALYST::isotope_list)
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 |
The rules how the spillover matrix is adapted
are explained in compCytof
.
An adapted spillover matrix with column and row names
according to out_chs
.
Helena Lucia Crowell helena.crowell@uzh.ch and Vito RT Zanotelli vito.zanotelli@uzh.ch
# 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)