addCodesetAnnotation: Add NanoString codeset annotation to an RccSet

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

Description

Returns a copy of the input RccSet where the codeset annotation has been merged into its fData slot. The merge key for each is a string formed from the concatenation of their CodeClass, GeneName, and Accession columns ("<CodeClass>_<GeneName>_<Accession>"). For creating the codeset annotation object, see buildCodesetAnnotation().

Usage

## S4 method for signature 'RccSet'
addCodesetAnnotation(rccSet, annot, reorder = TRUE,
  showWarnings = TRUE)

Arguments

rccSet	An RccSet object.
annot	Data frame containing the codeset annotation.
reorder	Logical indicating whether the probes should be reordered according to their barcodes (this can help in identifying barcode-specific artifacts – i.e. background noise).
showWarnings	Logical indicating whether or not warnings should be shown, if any.

Value

A copy of the input RccSet where the codeset annotation has been merged into its fData slot.

Author(s)

Dorothee Nickles, Robert Ziman

Examples

rccDir <- system.file("extdata", "RCC", package="NanoStringQCPro")
rccSet <- newRccSet(rccFiles = dir(rccDir, full.names=TRUE))
rlf <- system.file("extdata", "RLF", "NQCP_example.rlf", package="NanoStringQCPro")
annot <- buildCodesetAnnotation(rlf)
rccSet.annotated <- addCodesetAnnotation(rccSet, annot)

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