differentialAnalysis: differential analysis function based on DESeq2
In AlexHelloWorld/DifferentialAndSurvivalAnalysis:
Description
Usage
Arguments
Value
Description
Do differential analysis with DESeq2 recursively with attributes defined in 'fields' parameter
Usage
1
2
differentialAnalysis(countTable, coldata, fields, 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"
fields
name list of the attributes 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 list of DESeqDataSet object and output 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.
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Description Usage Arguments Value
Description
Do differential analysis with DESeq2 recursively with attributes defined in 'fields' parameter
Usage
1 2 | differentialAnalysis(countTable, coldata, fields, 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" |
fields |
name list of the attributes 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 list of DESeqDataSet object and output csv files for differential analysis results and vsd normalized expression table directly to current directory
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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