R/PhenTestResult.R

In PhenStat: Statistical analysis of phenotypic data

## Copyright © 2012-2014 EMBL - European Bioinformatics Institute
##
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
##
##     http://www.apache.org/licenses/LICENSE-2.0
##
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
##------------------------------------------------------------------------------
## PhenTestResult.R contains PhenTestResult function
##------------------------------------------------------------------------------
PhenTestResult <- function(model.output = NULL,
                           model.dataset = NULL,
                           depVariable = NULL,
                           refGenotype = NULL,
                           equation = "withWeight",
                           method = "MM",
                           model.effect.batch = NULL,
                           model.effect.variance = NULL,
                           model.effect.sex = NULL,
                           model.effect.interaction = NULL,
                           model.output.interaction = NULL,
                           model.effect.weight = NULL,
                           numberSexes = NULL,
                           pThreshold = 0.05,
                           model.formula.null = NULL,
                           model.formula.genotype = NULL,
                           model.output.genotype.nulltest.pVal = NULL,
                           model.output.quality = NULL,
                           model.output.summary = NULL,
                           model.output.averageRefGenotype = NULL,
                           model.output.percentageChanges = NULL)

## Construct PhenTestResult object from components

{
  x <- new("PhenTestResult", list(model.output = model.output))

  x$depVariable <- depVariable
  x$equation <- equation
  x$method <- method
  x$refGenotype <- refGenotype
  x$model.effect.batch <- model.effect.batch
  x$model.effect.variance <- model.effect.variance
  x$model.effect.sex <- model.effect.sex
  x$model.effect.interaction <- model.effect.interaction
  x$model.effect.weight <- model.effect.weight
  x$model.output.genotype.nulltest.pVal <-
    model.output.genotype.nulltest.pVal
  x$pThreshold <- pThreshold
  x$model.output <- model.output
  x$model.dataset <- model.dataset
  x$model.output.quality <- model.output.quality
  x$model.output.summary <- model.output.summary
  x$model.output.interaction <- model.output.interaction
  x$model.output.averageRefGenotype <-
    model.output.averageRefGenotype
  x$model.output.percentageChanges <-
    model.output.percentageChanges
  x
}
##------------------------------------------------------------------------------