RccSet-class {NanoStringQCPro} | R Documentation |
The RccSet class is a trivial extension of
ExpressionSet
, but with additional validation
criteria. RccSet
is a class generator function.
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 checkRccSet
, which provides additional checks and
generates warnings for unexpected or unusual conditions which, though
permitted by the class, may indicate data import errors.
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)