differentialAnalysisSingleAttribute: differential analysis function based on DESeq2 Do...

In AlexHelloWorld/DifferentialAndSurvivalAnalysis:

Description

differential analysis function based on DESeq2 Do differential analysis with DESeq2 on single attribute and two attribute

Usage

differentialAnalysisSingleAttribute(countTable, coldata, attribute, geneInfo,
  datasetIdentifier)

Arguments

countTable	a raw read count table
coldata	an annotation table for samples, must include attributes naming "barcode", "patient_barcode", "survival", "vital_status", "total_count", "cohort"
attribute	name of the attribute for differential expression analysis
geneInfo	an annotation table for genes, must include attribute nameing "gene_length"
datasetIdentifier	a prefix for the output csv files

Value

a DESeqDataSet object and output two csv files for differential analysis results and vsd normalized expression table directly to current directory

AlexHelloWorld/DifferentialAndSurvivalAnalysis documentation built on June 1, 2019, 3:51 a.m.