bioLOGIC-class: bioLOGIC
In decusInLabore/biologicSeqTools2: Seq Analysis Helper Functions

bioLOGIC-class

R Documentation

bioLOGIC

Description

This function defines the bioLOGIC data storage object

Arguments

`clusterSigEnrichmentList`	A list to store cluster signature enrichments
`documentationParams`	A list to store documentation parameters
`sampleDetailList`	A list to store sample details
`dbDetailList`	A list to store database login details
`projectDetailList`	A list to store project details
`scDetailList`	A list to store single-cell sample details
`referenceTableList`	A list to store reference tables
`dfGeneAnnotation`	A data.frame to store gene annotation information
`dfPCA`	A data.frame to store PCA results
`dfPCAgenes`	A data.frame to store PCA genes
`PCApercentVar`	A numeric vector to store PCA variation per dimension
`dfTPM`	A data.frame to store the TPM table
`dfFPKM`	A data.frame to store the TPM table
`RSEMcountMatrix`	A RSEM count matrix. Matrix.
`dfDesign`	A design data.frame. Should mimimally contain the columns sample.id, sample.group and dataseries. The ideal sample.id format is dataseries_sampleGroup_replicate. Example: WT_Treated0h_Rep1
`dfSummary`	A slot for the summary data.frame
`databaseTable`	Slot for a database table data.frame
`reportVec`	A character vector containing information for the report
`scriptVec`	A character vector containing details on used scripts
`GSEAtableList`	A list to store GSEA result tables
`documentationVector`	A character vector containing details for the documentation
`categoryViewTableList`	A list storing categoryView tables
`plotCollection`	A list to store plots
`ObjDds`	A slot to store a DESeq2 dds object
`DESeqNormReadCountsTable`	A data.frame for Normalised DEseq2 readcounts
`DEseq2contrastTable`	A data.frame to store the DESeq2 contrast result table
`DEseq2LRTtable`	A data.frame to store the DESeq2 LRT result table.
`enrichmentList`	A list for enrichment results
`dataTableList`	A list to store result tables