NanoStringDiff-class: NanoStringSet object and constructors

In Shedimus/NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data

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 <[e-mail]> chi wang <[e-mail]>

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))

Shedimus/NanoStringDiff documentation built on Dec. 5, 2019, 1:56 a.m.