This class contains the result of an RNA-Seq data analysis. The class contains
the transcript names together with the parameters per condition, i.e., overdispersion
and mean. Further it contains informative/non-informative values or p-values.
Objects from the Class
Objects can be created by calls of the form new("DEXUSResult", ...).
Slots
transcriptNames
The names of the transcripts, genes, exons, or regions of interest
sampleNames
The sample names as they were given in the input matrix.
inputData
The original read count matrix.
normalizedData
The normalized read count matrix.
sizeFactors
The size factors that were calculated for the normalization. This is that
factor that scales each column or sample.
INIValues
An informative/non-informative value for each sample that measures the evidence
for differential expression.
INIThreshold
The threshold for the I/NI values. Transcript with I/NI values above the
threshold will be considered as differentially expressed.
INICalls
A binary value for each transcript indicating whether it is differentially expressed.
pvals
In case of two known conditions or multiple known conditions it is possible to
calculate a p-value for each transcript. This value is given in this slot.
responsibilities
A matrix of the size of the input matrix. It indicates the condition
for each sample and transcript. The condition named "1" is the major condition. All other
conditions are minor conditions. In case of supervised (two known conditions or multiple
known conditions) analyses this clustering matrix will be the same for all transcripts.
posteriorProbs
An array of the dimension of transcripts times samples times conditions.
It gives the probability that a certain read count x was generated under a condition.
logFC
The log foldchanges between the conditions. The reference is always condition "1".
conditionSizes
The ratio of samples belonging to that condition.
These are the α_i values of the model.
sizeParameters
The size parameter estimates for each condition. These are the r_i values
of the model.
means
The mean of each condition. The μ_i values of the model.
dispersions
The dispersion estimates for each condition. The inverse size parameters.
params
The input parameters of the DEXUS algorithm.
Methods
[
Subsetting of a DEXUSResult.
as.data.frame
Converts the result object into a data frame.
conditionSizes
Returns the condition sizes or
α_i parameters of the model.
dispersions
Returns the dispersion, i.e. the inverse
size parameters, of the model.
INI
I/NI filtering of the result object.
INICalls
Returns a logical value
indication whether this transcript is differentially expressed or not.
INIThreshold
Returns the thresholds for the I/NI values.
INIThreshold<-
Sets the I/NI threshold. I/NI calls will be changed
accordingly.
INIValues
Returns the I/NI values.
inputData
Returns the input read counts.
logFC
Returns the log foldchange with respect to the first
condition.
means
Returns the mean per condition.
normalizedData
Returns the normalized data.
params
Returns a list of input parameters of DEXUS.
plot
Plots a heatmap of the read counts of the top genes.
posteriorProbs
Returns an array of posterior probabilities.
pvals
Returns the p-values per transcript in supervised mode.
responsibilities
Returns the clustering vector.
sampleNames
Returns the sample names.
show
Displays a data frame of results.
sizeFactors
Returns the size factors used for normalization.
sizeParameters
Returns the size parameters, i.e. the r_i values
of the model.
sort
Sorts the result object by I/NI values or p-values.
transcriptNames
Returns the transcript names.
Author(s)
Guenter Klambauer
Examples
showClass("DEXUSResult")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(dexus)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Attaching package: 'dexus'
The following object is masked from 'package:BiocGenerics':
sizeFactors
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dexus/DEXUSResult-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DEXUSResult-class
> ### Title: Class '"DEXUSResult"'
> ### Aliases: DEXUSResult-class conditionSizes,DEXUSResult-method
> ### dispersions,DEXUSResult-method INICalls,DEXUSResult-method
> ### INIThreshold,DEXUSResult-method INIThreshold<-,DEXUSResult-method
> ### INIValues,DEXUSResult-method inputData,DEXUSResult-method
> ### logFC,DEXUSResult-method means,DEXUSResult-method
> ### normalizedData,DEXUSResult-method params,DEXUSResult-method
> ### plot,DEXUSResult,missing-method posteriorProbs,DEXUSResult-method
> ### pvals,DEXUSResult-method responsibilities,DEXUSResult-method
> ### sampleNames,DEXUSResult-method show,DEXUSResult-method
> ### sizeFactors,DEXUSResult-method sizeParameters,DEXUSResult-method
> ### transcriptNames,DEXUSResult-method as.data.frame,DEXUSResult-method
> ### sort,DEXUSResult-method [,DEXUSResult,character-method
> ### [,DEXUSResult,numeric-method [,DEXUSResult,logical-method
> ### INI,DEXUSResult-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("DEXUSResult")
Class "DEXUSResult" [package "dexus"]
Slots:
Name: transcriptNames sampleNames inputData normalizedData
Class: character character matrix matrix
Name: sizeFactors INIValues INIThreshold INICalls
Class: numeric numeric numeric logical
Name: pvals responsibilities posteriorProbs logFC
Class: numeric matrix array matrix
Name: conditionSizes sizeParameters means dispersions
Class: matrix matrix matrix matrix
Name: params
Class: list
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.