Nothing
.DGEobjDef <- list(
# There are 4 immutable basetypes: row, col, assay, meta
# Each type must be one of these four basetypes
# Extensibility: Additional types can be added to .DGEobj$type as long as they are
# assigned to one of the 4 basetypes.
basetype = c(row = "row",
col = "col",
assay = "assay",
meta = "meta"),
# The value of type is a basetype.
# All types must be associated with one of the four basetypes.
type = c(row = "row",
col = "col",
assay = "assay",
meta = "meta",
geneData = "row",
exonData = "row",
isoformData = "row",
proteinData = "row",
affyData = "row",
granges = "row",
fit = "row",
contrast_fit = "row",
topTable = "row",
design = "col",
designMatrix = "col",
alignQC = "col",
counts = "assay",
intensities = "assay",
effectiveLength = "assay",
AffyRMA = "assay",
DGEList = "assay",
Elist = "assay",
isoformFrac = "assay",
corFit = "meta",
topTreat = "meta",
geneList = "meta", #intended for short gene lists
pathway = "meta", #should consider format standards for genelists and pathways
URL = "meta",
contrast_fit_treat = "meta",
contrastMatrix = "meta",
imputationMatrix = "meta",
#types with _orig suffix are intended to store the initialized data
#in its original state (i.e. before subsetting, normalizing)
counts_orig = "meta",
intensities_orig = "meta",
effectiveLength_orig = "meta",
geneData_orig = "meta",
exonData_orig = "meta",
isoformData_orig = "meta",
proteinData_orig = "meta",
granges_orig = "meta",
design_orig = "meta",
AffyRMA_orig = "meta",
svobj = "meta"
),
# These can only have one instance in a DGEobj
uniqueType = c("counts",
"counts_orig",
"design",
"design_orig",
"intensities",
"intensities_orig",
"geneData",
"geneData_orig",
"exonData",
"exonData_orig",
"isoformData",
"isoformData_orig",
"proteinDaa",
"proteinData_orig",
"effectiveLength",
"effectiveLength_orig",
"granges",
"granges_orig",
"AffyRMA",
"AffyRMA_orig"
),
allowedLevels = c("gene", "exon", "isoform", "protein", "affy"),
primaryAssayNames = c(gene = "counts",
exon = "counts",
isoform = "intensities",
protein = "intensities",
affy = "AffyRMA")
)
class(.DGEobjDef) <- "DGEobjDef"
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