ezMethodDEXSeqAnalysis: RunMethod for reference class EzAppDEXSeqAnalysis

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

RunMethod for reference class EzAppDEXSeqAnalysis

Description

Differential exon usage is assessed using the same steps that are done in the wrapper function DEXSeq from the DEXSeq package. The wrapper is not used here, because dispersion plots and MA-plots are integrated in the report and those cannot be produced from the resulting object of the wrapper function. The following steps are done in the analysis

• DEXSeqDataSetFromHTSeq: instantiates a DEXSeqDataSet object

• estimateSizeFactors: normalizes to account for different coverage

• estimateDispersions: assesses variability within and between experimental groups

• testForDEU: getting fdr statistics for deu

• estimateExonFoldChanges: fold changes are estimated

Once these steps are done the results are written to a report.

Usage

ezMethodDEXSeqAnalysis(input = NA, output = NA, param = NA)

Arguments

input	EzDataSet reference object specifying input
output	EzDataSet reference object specifying output
param	EzParam reference object specifying additional parameters

Details

Before running the DEU-analysis, it is verified that count data is available. It is expected that the current working directory contains files with the same name as the BAM-files specified in the input, but with a file-extension that can be specified and which defaults to 'count'. In case, the count files are not available they are generated using the function DEXSeqCounting.

uzh/ezRun documentation built on April 24, 2024, 4:01 p.m.