anota2seqGetQualityControl {anota2seq} | R Documentation |
Retrieves the anota2seqPerformQC output from the Anota2seqDataSet
anota2seqGetQualityControl(object) ## S4 method for signature 'Anota2seqDataSet' anota2seqGetQualityControl(object)
object |
An Anota2seqDataSet. |
The function outputs a list containing the following data:
omniIntStats: A matrix with a summary of the statistics from the omnibus interaction analysis containing the following columns:
intMS: the mean square for the interaction;
intDf: the degrees of freedom for the interaction;
residMS: the residual error mean square;
residDf: the degrees of freedom for the residual error;
residMSRvm: the mean square for the residual error after applying RVM;
residDfRvm: the degrees of freedom for the residual error after applying RVM;
intRvmFval: the F-value for the RVM statistics;
intP: the p-value for the interaction;
intRvmP: the p-value for the interaction using RVM statistics;
intPAdj: the adjusted [for multiple testing using the selected multiple testing correction method] p-value of the interaction;
intRvmPAdj: the adjusted [for multiple testing using the selected multiple testing correction method] p-value of the interaction using RVM statistics).
omniGroupStats: A matrix with a summary of the statistics from the omnibus treatment analysis containing the following columns:
groupSlope: the common slope used in APV;
groupSlopeP: if the slope is <0 or >1 a p-value for the slope being <0 or >1 is calculated; if the slope is >=0 & <=1 this value is set to 1;
groupMS: the mean square for treatments;
groupDf: the degrees of freedom for the treatments;
groupResidMS: the residual error mean square);
groupResidDf: the degrees of freedom for the residual error;
residMSRvm: the mean square for the residual error after applying RVM;
groupResidDfRvm: the degrees of freedom for the residual error after applying RVM;
groupRvmFval: the F-value for the RVM statistics;
groupP: the p-value for the sample class effect;
groupRvmP: the p-value for the sample class effect using RVM statistics;
groupPAdj: the adjusted [for multiple testing using the selected multiple testing correction method] p-value of the sample class effect);
groupRvmPAdj: the adjusted [for multiple testing using the selected multiple testing correction method] p-value of the sample class effect using RVM statistics).
groupIntercepts A matrix with the group intercepts, i.e. the translational activity for each group independent of cytosolic mRNA level. Can be used for e.g. clustering of translational activity.
correctionMethod: The multiple testing correction method used to adjust the nominal p-values.
dsfSummary: A vector with the obtained frequencies of outlier dfbetas without the interaction term in the model.
dfbetas: A matrix with the dfbetas from the model without the interaction term in the model.
residuals: The residuals from the regressions without the interaction term in the model.
fittedValues: A matrix with the fitted values from the regressions without the interaction term in the model.
phenoClasses: The sample classes used in the analysis. The sample class order can be used to create the contrast matrix when using anota2seqRun or anota2seqAnalyze.
sampleNames: A vector with the sample names (from the translated mRNA [e.g. polysome-associated mRNA or RPF] samples).
abParametersInt: The ab parameters for the inverse gamma fit for the interactions within RVM.
abParametersGroup: The ab parameters for the inverse gamma fit for treatments within RVM.
See Also as anota2seqPerformQC
data(anota2seq_data) #Initialize Anota2seqDataSet Anota2seqDataSet <- anota2seqDataSetFromMatrix( dataP = anota2seq_data_P[1:100,], dataT = anota2seq_data_T[1:100,], phenoVec = anota2seq_pheno_vec, dataType = "RNAseq", normalize = TRUE) #Run QC Anota2seqDataSet <- anota2seqPerformQC(Anota2seqDataSet) #Get QC qc <- anota2seqGetQualityControl(Anota2seqDataSet)