uRNAList: uRNAList - class

In AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

Description

A list-based class (similar to the RGList class in limma package) for the storing of Agilent chips microRNA data uRNAList objects are created by read.agiMicroRna

uRNAList Components

uRNAList objects are created by new("uRNAList",Newagi) where Newagi is a list. with the following components:

uRNAList\$TGS

matrix, 'gTotalGeneSignal'

uRNAList\$TPS

matrix, 'gTotalProbeSignal'

uRNAList\$meanS

matrix, 'gMeanSignal'

uRNAList\$procS

matrix, 'gProcessedSignal'

uRNAList\$targets

data.frame, 'FileName'

uRNAList\$genes\$ProbeName

vector of characters, 'AGilent Probe Name'

uRNAList\$genes\$GeneName

vector of characters, 'microRNA Name'

uRNAList\$genes\$ControlType

vector of integers, '0'= Feature, '1'= Positive control, '-1'= Negative control

uRNAList\$other\$gIsGeneDetected

matrix, FLAG to classify signal if 'IsGeneDetected=1' or 'not=0'

uRNAList\$other\$gIsSaturated

matrix, FLAG to classify signal if 'IsSaturated = 1' or 'not=0'

uRNAList\$other\$gIsFeatPopnOL

matrix, FLAG to classify signal if 'IsFeatPopnOL = 0' or 'not=1'

uRNAList\$other\$gIsFeatNonUnifOL

matrix, FLAG to classify signal if 'gIsFeatNonUnifOL = 0' or 'not=1'

uRNAList\$other\$gBGMedianSignal

matrix, gBGMedianSignal

uRNAList\$other\$gBGUsed

matrix, gBGUsed

Author(s)

Pedro Lopez-Romero

Examples

## Not run: 
    data(dd.micro)

## End(Not run)

AgiMicroRna documentation built on Nov. 8, 2020, 5:25 p.m.