Description Usage Arguments Value
differential analysis function based on DESeq2 Do differential analysis with DESeq2 on single attribute and two attribute
1 2 | differentialAnalysisSingleAttribute(countTable, coldata, attribute, geneInfo,
datasetIdentifier)
|
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 |
a DESeqDataSet
object and output two csv files for differential analysis results and vsd normalized expression table directly to current directory
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