csDEXdataSet-class: Class '"csDEXdataSet"'

In mstrazar/csDEX: Condition-specific differential exon expression.

Description

A data structure with the features-by-condition matrix, storing the expression values for percentage-spliced in or read counts, along with metadata for both rows and columns. Optionally, gene expression is stored as counts-per-million reads (CPM).

Objects from the Class

Objects can be created by calls of the form new("csDEXdataSet", ...).

Slots

dataType:

Object of class "character" Either "PSI" (percentage-spliced in) or "count" (read counts), determining the underlying data distribution.

exprData:

Object of class "matrix" Feature-by-condition matrix containing expression data.

rowData:

Object of class "data.frame" Row (feature) metadata.

colData:

Object of class "data.frame" Column (condition) metadata, the experiment design.

cpmData:

Object of class "matrix" Optional. Counts-per-million reads (CPM) associated to a group (gene).

Methods

dataType

signature(obj = "csDEXdataSet"): The accessor (getter) of the csDEXdataSet object data type (PSI or count).

colData

signature(obj = "csDEXdataSet"): The accessor (getter) of column (condition) metadata provided by the experiment design file.

colData<-

signature(obj = "csDEXdataSet"): The accessor (setter) of column (condition) metadata provided by the experiment design file.

cpmData

signature(obj = "csDEXdataSet"): The accessor (getter) of the counts per million reads (CPM) associated to each gene (groupID). Computable if the input.read.count field is set and provided in the experiment design file.

cpmData<-

signature(obj = "csDEXdataSet"): The accessor (setter) of the counts per million reads (CPM) associated to each gene (groupID).

exprData

signature(obj = "csDEXdataSet"): The accessor (getter) of the expression data matrix constructed by merging the experimental data in samples.

exprData<-

signature(obj = "csDEXdataSet"): The accessor (setter) of the expression data matrix constructed by merging the experimental data in samples.

rowData

signature(obj = "csDEXdataSet"): The accessor (getter) of row (feature) metadata provided by the experiment data files.

rowData<-

signature(obj = "csDEXdataSet"): The accessor (setter) of row (feature) metadata provided by the experiment data files.

estimatePrecisions

signature(obj = "csDEXdataSet"): Estimate the precisions hyperparameter for each feature by using the external edgeR::estimateDisp function. Required for fitting read-count based models. The function estimateSizeFactors should be called on the cdx object prior to estimatePrecisions call.

estimateGeneCPM

signature(obj = "csDEXdataSet"): Estimate counts per million reads (CPM) associated to each gene (groupID). An integer field named input.read.count is required in the design file, specifying the sequencing depth measured by the number of sequenced reads / read pairs. Can be used by both PSI and count models to skip testing for low-expressed genes and avoid Type I errors that are dut to changes in gene expression (and not differential splicing).

estimateSizeFactors

signature(obj = "csDEXdataSet"): Estimate the size factors hyperparameter for each feature by using the external DESeq2::estimateSizeFactorsForMatrix function. Required for normalization of samples with respect to sequencing depth and mandatory when fitting count models.

Examples

showClass("csDEXdataSet")

mstrazar/csDEX documentation built on May 23, 2019, 8:16 a.m.