NanoStringDiff-class: NanoStringSet object and constructors

Description Usage Arguments Value Methods Author(s) See Also Examples

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

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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

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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.