anota2seqGetNormalizedData: Accessor for the 'normalizedDataP' and 'normalizedDataT'...

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

Description

Retrieve the data that is used in the analysis (i.e. if raw RNAseq counts were supplied, this function retrieves the normalized counts used in the analysis).

Usage

anota2seqGetNormalizedData(object)

## S4 method for signature 'Anota2seqDataSet'
anota2seqGetNormalizedData(object)

Arguments

object

A Anota2seqDataSet.

Value

A list of 2 elements named "dataP" and "dataT" containing the corresponding normalized data to be used for the analysis. Note that dataT and dataP have the same sample order such that e.g. column 1 in dataP is the translated mRNA data for a sample, column 1 in dataT is the total mRNA data.

See Also

Anota2seqDataSet-class

Examples

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)
# Get normalized dataP
normDataP <- anota2seqGetNormalizedData(Anota2seqDataSet)[["dataP"]]
head(normDataP)

anota2seq documentation built on Nov. 8, 2020, 6 p.m.