NanoStringSet-class {NanoStringDiff} | R Documentation

## NanoStringSet object and constructors

### Description

The `NanoStringSet` is a s4 class used to store data from NanoString nCounter analyzer. This class a subclass of `ExpressionSet`, with six more slots: positiveControl, negativeControl, housekeepingControl, positiveFactor, negativeFactor and housekeepingFactor. The constructor functions `createNanoStringSet` and `createNanoStringSetFromCsv` create a NanoStringSet object from two types of input: seperate matrix or csv files. See the vignette for examples of contruction from these two input types.

### Usage

    createNanoStringSet(endogenous,positiveControl,negativeControl,
                     housekeepingControl,designs)

    createNanoStringSetFromCsv(path, header=TRUE, designs)

### Arguments

`endogenous` | for matrix input: a matrix of non-negative integers of endogenes
`positiveControl` | for matrix input: a matrix of non-negative integers of positive control genes. There must have 6 positive control genes order by concentrations form high to low
`negativeControl` | for matrix input: a matrix of non-negative integers of negative control genes
`housekeepingControl` | for matrix input: a matrix of non-negative integers of housekeeping control genes
`designs` | for data.frame input: phenotype data for NanoString nCounter data with at least one column. Each row is one sample, that is the number of rows must equal number of samples or replicates in the data.
`path` | path to the csv file.
`header` | a logical value indicating whether the file contains the names of the variables as its first line. The default value is TRUE.

### Value

A NanoStringSet object.

### Methods

positiveControl, positiveControl<- :

  Access and set positive control genes.

negativeControl, negativeControl<- :

  Access and set negative control genes.

housekeepingControl, housekeepingControl<- :

  Access and set housekeeping control genes.

positiveFactor, positiveFactor<- :

  Access and set positive factors.

negativeFactor, negativeFactor<- :

  Access and set negative factors.

housekeepingFactor, housekeepingFactor<- :

  Access and set housekeeping factors.

### Author(s)

hong wang <hong.wang@uky.edu> chi wang <chi.wang@uky.edu>

### See Also

positiveControl, negativeControl, housekeepingControl, positiveFactor, negativeFactor, housekeepingFactor

### Examples

    endogenous=matrix(rpois(100,50),25,4)
    positive=matrix(rpois(24,c(128,32,8,2,0.5,0.125)*80),6,4)
    negative=matrix(rpois(32,10),8,4)
    housekeeping=matrix(rpois(12,100),3,4)
    designs=data.frame(group=c(0,0,1,1),gender=c("male","female","female","male"),
    age=c(20,40,39,37))
    NanoStringData=createNanoStringSet(endogenous,positive,negative,
                                    housekeeping,designs)
    NanoStringData
    pData(NanoStringData)
    positiveControl(NanoStringData)
    head(exprs(NanoStringData))

[Package NanoStringDiff version 1.9.2 Index]