newRccSet: Create a new RccSet object

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

Description

This is the main wrapper function for generating an RccSet from NanoString data. The function takes as input a vector of NanoString .RCC files with the raw data or a .CSV file generated via the RCC Collector Tool Export feature of NanoString's nSolver Analysis Software, an optional path to the .RLF file describing the codeset used, optional paths to additional annotation about the features and samples, and details about the experiment. It returns an RccSet object.

Usage

newRccSet(rccFiles, rccCollectorToolExport = NULL, rlf = NULL,
  cdrDesignData = NULL, extraPdata = NULL, blankLabel = "blank",
  addEgAnnotations = FALSE, dropPdataCols = c("FileVersion",
  "SoftwareVersion", "Owner", "SystemAPF", "ScannerID", "CartridgeBarcode"),
  dropFdataCols = c("CodeClass_codesetAnnot", "Accession_codesetAnnot",
  "GeneName_codesetAnnot", "Accession_CDR"), experimentData.name = "",
  experimentData.lab = "", experimentData.contact = "",
  experimentData.title = "", experimentData.abstract = "",
  experimentData.url = "", experimentData.other = list())

Arguments

rccFiles	Vector of paths to .RCC files with the raw count data.
rccCollectorToolExport	Path to a .CSV file generated via the RCC Collector Tool Export feature of NanoString's nSolver Analysis Software. (Note that this is an alternative to rccFiles, and if both arguments are specified at the same time, the function will throw an error.)
rlf	Path to the NanoString .RLF file describing the codeset used in generating the .RCCs.
cdrDesignData	Path to a .CSV extract of the "Design Data" tab of a CDR spreadsheet corresponding to the rest of the input files. See 'Details' section of the buildCodesetAnnotation() help page for more info on how this extract should be prepared.
extraPdata	Vector of paths to files containing additional annotation about the samples which will be added to the phenoData of the output RccSet. All files should be tab-separated and should contain a column labelled "FileName" whose values correspond exactly to the basenames (including .RCC extension) of the files specified in rccFiles or listed in the RCC Collector Tool Export. More than one such file may be used. A SampleType column should be present in at most one file.
blankLabel	Value for the output's phenoData SampleType column that will indicate blank samples. This will be recorded in the varMetadata for SampleType. Blank samples, if available, play an important role in preprocessing.
addEgAnnotations	Logical indicating whether or not to add EntrezGene annotations from the org.Hs.eg.db package.
dropPdataCols	Character vector specifying phenoData columns to be dropped from the output object (if empty or NULL, no columns will be dropped).
dropFdataCols	Character vector specifying featureData columns to be dropped from the output object (if empty or NULL, no columns will be dropped).
experimentData.name	String passed to the 'name' slot of the output RccSet's experimentData.
experimentData.lab	String passed to the 'lab' slot of the output RccSet's experimentData.
experimentData.contact	String passed to the 'contact' slot of the output RccSet's experimentData.
experimentData.title	String passed to the 'title' slot of the output RccSet's experimentData.
experimentData.abstract	String passed to the 'abstract' slot of the output RccSet's experimentData.
experimentData.url	String passed to the 'url' slot of the output RccSet's experimentData.
experimentData.other	List passed to the 'other' slot of the output RccSet's experimentData.

Details

In the .RLF (and sometimes in the .RCC files), the GeneName field for positive and negative control probes contains a parenthesized label indicating the RNA “spike-in” levels for each probe. These labels are removed from the control probe GeneNames in the output and recorded instead in SpikeInInput in the output's featureData.

A pseudocount of 1 is added to all measurements to enable subsequent log transformation of the data.

If the phenoData SampleType column is not specified via an annotation file passed in through extraPdata, it will be created and assigned NA for all samples.

Value

An RccSet containing the raw NanoString data and annotations.

Author(s)

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"),
    extraPdata = system.file("extdata", "extraPdata", "SampleType.txt", package="NanoStringQCPro"),
    blankLabel = "blank",
    experimentData.name = "Robert Ziman",
    experimentData.lab = "Richard Bourgon",
    experimentData.contact = "[e-mail]",
    experimentData.title = "NanoStringQCPro example dataset",
    experimentData.abstract = "Example data for the NanoStringQCPro package"
)

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