Fit a channel-units to assigned-units calibration from a bead acquisition

A BEAD FILE IS NAMED BY DETECTOR. Beads carry no antibody, so a bead file usually has no $PnS and its channels resolve to detector names (FITC-A) where the samples resolve to markers (CD3). The assigned-value table may therefore name either: a marker symbol, or a detector as $PnN writes it. With channel_names supplied, a detector name is looked up there, and the detector each row was fitted on is returned in channel, so the fit is applied to the samples by detector ($PnN names the detector, Spidlen et al. 2010) rather than by a stain name the bead file does not have.

Usage

fit_bead_calibration(
  bead_exprs,
  channel_cols,
  assigned,
  min_r2 = 0.98,
  channel_names = NULL
)

Arguments

bead_exprs

the bead file's expression matrix, linear units

channel_cols

named integer vector, marker or channel name to column

assigned

data.frame with a marker column and one column per bead population, or a long form carrying marker, peak and value

min_r2

fit quality below which a channel is reported as not calibrated

channel_names

the bead file's $PnN values, as read, or NULL.

Value

a data.frame, one row per channel