DEXUSResult-class: Class '"DEXUSResult"'

In dexus: DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates

Description

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")

dexus documentation built on Nov. 8, 2020, 11:08 p.m.