RPPASetSummary-class {RPPASPACE}

Class “RPPASetSummary”

Description

The RPPASetSummary class contains the summary information derived from an RPPASet object.

Usage

RPPASetSummary(rppaset,
               onlynormqcgood=ran.prefitqc(rppaset))
is.RPPASetSummary(x)
## S4 method for signature 'RPPASetSummary'
write.summary(object,
              path,
              prefix="rppaspace",
              ...)

Arguments

rppaset

object of class RPPASet

onlynormqcgood

logical scalar. If TRUE, filters the slides to be normalized according to their pre-fit quality control scores.

x

object of class RPPASetSummary

object

object of class RPPASetSummary

path

character string specifying the path from the current directory to the directory containing the files to be processed

prefix

character string used as a prefix on files generated by the write.summary method

...

extra arguments for generic routines

Value

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.

Objects from the Class

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.

Slots

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

Methods

write.summary

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).

Note

The three CSV files may be reordered (to match that of the original input) when written to disk.

Author(s)

P. Roebuck [e-mail], James M. Melott [e-mail]

See Also

RPPASet