RccSet-class: RccSet class, derived from ExpressionSet

In NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data

Description

The RccSet class is a trivial extension of ExpressionSet, but with additional validation criteria. RccSet is a class generator function.

Details

A valid RccSet object must have the following columns in featureData: "CodeClass", "GeneName", and "Accession". It must also have the following phenoData columns: "FileName", "SampleID", "LaneID", "FovCount", "FovCounted", "StagePosition", "BindingDensity", "CartridgeID", and "SampleType". A final requirement is that the "FovCount" column of phenoData have at most one distinct value.

See Also

See checkRccSet, which provides additional checks and generates warnings for unexpected or unusual conditions which, though permitted by the class, may indicate data import errors.

Examples

data("example_rccSet")
e <- example_rccSet

# "ExpressionSet" constructor makes a new assayData environment
r1 <- RccSet(e)
validObject(r1)
assayData(e)
assayData(r1)
head(pData(r1))
head(fData(r1))

# For other constructors, if not explicitly supplied, blank phenoData and
# featureData objects are populated with mandatory columns (and NA values).
r2 <- RccSet(assayData(e))
validObject(r2)
head(pData(r2))
head(fData(r2))

r3 <- RccSet(assayData(e), phenoData(e), featureData(e))
identical(pData(r1), pData(r3))
identical(fData(r1), fData(r3))
identical(annotation(r1), annotation(r3)) # We forgot it!
annotation(e)
r3 <- RccSet(assayData(e), phenoData(e), featureData(e), annotation = annotation(e))
identical(annotation(r1), annotation(r3)) # Better
identical(r1, r3) # False, due to assayData environments
assayData(r1)
assayData(r3)

# Matrix contructor is similar
r4 <- RccSet(exprs(e), phenoData(e), featureData(e), annotation = annotation(e))
identical(exprs(r1), exprs(r4))

# Blank object constructor
r0 <- RccSet()
dim(r0)
pData(r0)
fData(r0)

NanoStringQCPro documentation built on Nov. 8, 2020, 8:11 p.m.