tRanslatome (version 1.10.0)

TranslatomeDataset-class: Class TranslatomeDataset

Description

A class generated from the function newTranslatomeDataset() containing the input matrix, the condition vectors and labels and the result of the differential expression analysis at the two expression levels. This class represents an analysis in its entirety, containing all data from input parameters to output results.

Slots

expr.matrix:

Object of class matrix specifying the normalized signal intensity data, each row representing a gene and each column representing a sample.

cond.a:

Object of class character specifying a vector of column names belonging to expression matrix. These columns contain the signal intensity data coming from the samples of the first expression level of the control condition.

cond.b:

Object of class character specifying a vector of column names belonging to expression matrix. These columns contain the signal intensity data coming from the samples of the first expression level of the treatment condition.

cond.c:

Object of class character specifying a vector of column names belonging to expression matrix. These columns contain the signal intensity data coming from the samples of the second expression level of the control condition.

cond.d:

Object of class character specifying a vector of column names belonging to expression matrix. These columns contain the signal intensity data coming from the samples of the second expression level of the treatment condition.

data.type:

Object of class character specifying the type of the data contained in exprMatrix. The default is "array" and the alternative is "ngs".

label.condition:

Object of class character specifying the names given to the two conditions. By default, these values are "control" and "treated", but user can specify others.

label.level:

Object of class character specifying the names given to the two levels. By default levels are named "1st level" and "2nd level", but the user can specify others.

DEGs:

Object of class DEGs specifying the result of the differential expression analysis at the two expression levels.

Accessors

getExprMatrix

signature(object = "TranslatomeDataset"): displays anObject of class matrix specifying the normalized signal intensity data, each row representing a gene and each column representing a sample.

getConditionA

signature(object = "TranslatomeDataset"): displays anObject of class character specifying a vector of column names belonging to expression matrix. These columns contain the signal intensity data coming from the samples of the first expression level of the control condition.

getConditionB

signature(object = "TranslatomeDataset"): displays anObject of class character specifying a vector of column names belonging to expression matrix. These columns contain the signal intensity data coming from the samples of the first expression level of the treatment condition.

getConditionC

signature(object = "TranslatomeDataset"): displays anObject of class character specifying a vector of column names belonging to expression matrix. These columns contain the signal intensity data coming from the samples of the second expression level of the control condition.

getConditionD

signature(object = "TranslatomeDataset"): displays anObject of class character specifying a vector of column names belonging to expression matrix. These columns contain the signal intensity data coming from the samples of the second expression level of the treatment condition.

getDataType

signature(object = "TranslatomeDataset"): displays anObject of class character specifying the type of the data contained in exprMatrix. The default is "array" and the alternative is "ngs".

getConditionLabels

signature(object = "TranslatomeDataset"): displays anObject of class character specifying the names given to the two conditions. By default, these values are "control" and "treated", but user can specify others.

getLevelLabels

signature(object = "TranslatomeDataset"): displays anObject of class character specifying the names given to the two levels. By default levels are named "1st level" and "2nd level", but the user can specify others.

getDEGs

signature(object = "TranslatomeDataset"): displays anObject of class DEGs specifying the result of the differential expression analysis at the two expression levels.

Methods

computeDEGs

signature(object = "TranslatomeDataset"): compute the differentially expressed genes at the two levels by means of the chosen method, returning anObject of class DEGs.

show

signature(object = "TranslatomeDataset"): displays all the slots of the class.

See Also

TranslatomeDataset newTranslatomeDataset computeDEGs

Examples

showClass("TranslatomeDataset")