anota2seqGetResidOutlierTest: Retrieve residOutlierTest

In ChrOertlin/anota2seq: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Description

Retrieves the output of the anota2seqResidualOutlierTest function from the Anota2seqDataSet.

Usage

anota2seqGetResidOutlierTest(object)

## S4 method for signature 'Anota2seqDataSet'
anota2seqGetResidOutlierTest(object)

Arguments

object

An Anota2seqDataSet.

Value

A list with the following items:

• confInt: The selected confInt (see function arguments).

• rnormIter: The number of sampled data sets.

• outlierMatrixLog: A logical matrix describing which residuals were outliers in the last iteration of the analysis.

• meanOutlierPerIteration: The fraction outliers per iteration.

• obtainedComparedToExpected: The ratio of the expected number of outlier residuals compared to the expected number of outliers given the selected confInt.

• nExpected Number of expected outlier residuals.

• nObtained Number of obtained outliers residuals.

See Also

anota2seqResidOutlierTest

Examples

data(anota2seq_data)
Anota2seqDataSet <- anota2seqDataSetFromMatrix(
    dataP = anota2seq_data_P[1:100,],
    dataT = anota2seq_data_T[1:100,],
    phenoVec = anota2seq_pheno_vec,
    dataType = "RNAseq",
    normalize = TRUE)
# Run QC, it is mandatory for anota2seqResidualOutlierTest
Anota2seqDataSet <- anota2seqPerformQC(Anota2seqDataSet)
# Run the Residual outlier testing
Anota2seqDataSet <- anota2seqResidOutlierTest(Anota2seqDataSet)

#Get resdidual outlier testing
rot <- anota2seqGetResidOutlierTest(Anota2seqDataSet)

ChrOertlin/anota2seq documentation built on Aug. 4, 2021, 2:17 p.m.