The RPPASetSummary class contains the summary information derived from an RPPASet object.
RPPASetSummary(rppaset,
onlynormqcgood=ran.prefitqc(rppaset))
is.RPPASetSummary(x)
# S4 method for RPPASetSummary
write.summary(object,
path,
prefix="rppaspace",
...)The RPPASetSummary generator returns an object of class
RPPASetSummary.
The is.RPPASetSummary method returns TRUE if its
argument is an object of class RPPASetSummary.
The write.summary method invisibly returns NULL.
object of class RPPASet
logical scalar. If TRUE, filters the slides
to be normalized according to their pre-fit quality control scores.
object of class RPPASetSummary
object of class RPPASetSummary
character string specifying the path from the current directory to the directory containing the files to be processed
character string used as a prefix on files generated by
the write.summary method
extra arguments for generic routines
Although objects of the class can (in theory) be created by a direct call
to new, the only realistic method is to use the
RPPASetSummary generator function.
raw:numeric matrix of raw concentrations
ss:numeric matrix of \(R^2\) statistical values
norm:numeric matrix of normalized concentrations
probs:numeric vector of goodness of fit probabilities,
or NULL (if pre-fit QC analysis was not requested)
completed:logical matrix specifying stage completion for each slide
noise:numeric vector of calculated log concentrations for noise qc values for positive control dilution series with Spot.Types designated as posCtrl-Noise or Noise.
design:object of class RPPADesignParams, common to all
the slides
onlynormqcgood:logical scalar specifying if raw concentrations were filtered according to their pre-fit quality control scores prior to normalization
version:character string containing the version of this package used to construct the object
signature(object = "RPPASetSummary"):
Potentially generates multiple CSV and TSV files: one for the raw concentrations (rppaspace_conc_raw.csv"), one for the \(R^2\) statistics (rppaspace_ss_ratio.csv), and one for the normalized concentrations (rppaspace_conc_norm_[norm_method].csv); a fourth file containing the goodness of fit probabilities (rppaspace_prefit_qc.csv) may be present if pre-fit QC analysis was requested. If spatial adjustments were requested, a TSV file (spatial_adjustments.tsv) will be created. If positive control dilution series have been declared as Noise or PosCtrl-Noise points in the design file, an additional CSV file of noise statistics will be created (rppaspace_noise.csv). If prefit QC analysis was done and/or noise qc metric were created, a combined qc metrics file will be created (rppaspace_combined_qc.csv) as well. Additionally, a TSV file detailing completion of each stage of processing for each slide is produced (rppaspace_summary.tsv).
P. Roebuck paul_roebuck@comcast.net, James M. Melott jmmelott@mdanderson.org
RPPASet