DEGs-class {tRanslatome} | R Documentation

## Class `DEGs`

### Description

A class generated from the function `computeDEGs()` containing the result of the differential expression analysis at the two expression levels.

### Slots

`DEGs.table`:

  Object of class `matrix` containing all the differential expression analysis. The matrix contains one row for each gene, while columns are organized as follows:

  1. `log2 FC(1st level)`, log2 fold change in the first level,

  2. `avg(1st level,control)`, average signal intensities of the control samples in the first level,

  3. `sd(1st level,control)`, standard deviation of the signal intensities of the control samples in the first level,

  4. `avg(1st level,treated)`, average signal intensities of the treated samples in the first level,

  5. `sd(1st level,treated)`, standard deviation of the signal intensities of the treated samples in the first level,

  6. `pv.METHOD(1st level)`, the differential expression p-value returned from the chosen method in the first level (the name of this column will change according to the selected method),

  7. `pv.METHOD.BH(1st level)`, the Benjamini-Hochberg corrected differential expression p-value returned from the chosen method in the first level (the name of this column will change according to the selected method),

  8. `log2 FC(2nd level)`, log2 fold change in the second level,

  9. `avg(2nd level,control)`, average signal intensities of the control samples in the second level,

  10. `sd(2nd level,control)`, standard deviation of the signal intensities of the control samples in the second level,

  11. `avg(2nd level,treated)`, average signal intensities of the treated samples in the second level,

  12. `sd(2nd level,treated)`, standard deviation of the signal intensities of the treated samples in the second level,

  13. `pv.METHOD(2nd level)`, the differential expression p-value returned from the chosen method in the second level (the name of this column will change according to the selected method),

  14. `pv.METHOD.BH(2nd level)`, the Benjamini-Hochberg corrected differential expression p-value returned from the chosen method in the second level (the name of this column will change according to the selected method),

  15. `level1Up`, boolean value set to 1 if the gene is upregulated in the first level, otherwise set to 0,

  16. `level1Down`, boolean value set to 1 if the gene is downregulated in the first level, otherwise set to 0,

  17. `level2Up`, boolean value set to 1 if the gene is upregulated in the second level, otherwise set to 0,

  18. `level2Down`, boolean value set to 1 if the gene is downregulated in the second level, otherwise set to 0,

  19. `DownDown`, boolean value set to 1 if the gene is downregulated in both levels, otherwise set to 0,

  20. `DownUp`, boolean value set to 1 if the gene is downregulated in the first level and up regulated in the second level, otherwise set to 0,

  21. `UpDown`, boolean value set to 1 if the gene is upregulated in the first level and downregulated in the second level, otherwise set to 0,

  22. `UpUp`, boolean value set to 1 if the gene is upregulated in both levels, otherwise set to 0

`method`:

  Object of class `character` specifying the statistical method used to detect DEGs.

`significance.threshold`:

  Object of class `numeric` specifying the significance threshold used to detect DEGs.

`FC.threshold`:

  Object of class `numeric` specifying the fold change threshold used to detect DEGs.

`label.level.DEGs`:

  Object of class `character` specifying the names of the two levels compared in the experiment.

`label.condition`:

  Object of class `character` specifying the names of the two conditions compared in the experiment.

### Accessors

getDEGsMethod

  `signature(object = "DEGs")`: displays an object of class `character` specifying the statistical method used to detect DEGs.

significance.threshold

  `signature(object = "DEGs")`: displays an object of class `numeric` specifying the significance threshold used to detect DEGs.

FC.threshold

  `signature(object = "DEGs")`: displays an object of class `numeric` specifying the fold change threshold used to detect DEGs.

label.level.DEGs

  `signature(object = "DEGs")`: displays an object of class `character` specifying the names of the two levels compared in the experiment.

label.condition

  `signature(object = "DEGs")`: displays an object of class `character` specifying the names of the two conditions compared in the experiment.

DEGs.table

  `signature(object = "DEGs")`: displays an object of class `matrix` specifying the table of computed DEGs.

### Methods

CVplot

  `signature(object = "DEGs")`: enables the generation of a plot where, for each level, signal coefficients of variation for each gene are displayed against their log2 fold changes. DEGs are color labeled.

GOEnrichment

  `signature(object = "DEGs")`: enables the GO enrichment analysis of the differentially expressed genes at each level.

RegulatoryEnrichment

  `signature(object = "DEGs")`: enables the enrichment analysis of post-transcriptional regulators (RBPs, miRNAs, ecc) in the DEGs gene list, by means of Fisher test.

Histogram

  `signature(object = "DEGs")`: enables the generation of a histogram displaying the number of DEGs belonging to different classes according to their expression behaviour at the two levels.

MAplot

  `signature(object = "DEGs")`: enables the generation of a plot where, for each level, average signal intensities for each gene are displayed against their log2 fold changes. DEGs are color labeled.

Scatterplot

  `signature(object = "DEGs")`: enables the generation of a plot where fold changes at the first level are displayed for each gene against fold changes at the second level. DEGs are color labeled.

SDplot

  `signature(object = "DEGs")`: enables the generation of a plot where, for each level, signal standard deviations for each gene are displayed against their log2 fold changes. DEGs are color labeled.

show

  `signature(object = "DEGs")`: displays all the six slots of the class.

### Author(s)

Toma Tebaldi, Erik Dassi, Galena Kostoska

### See Also

`TranslatomeDataset` `computeDEGs` `RegulatoryEnrichment` `GOEnrichment` `EnrichedSets` `GOsets`

### Examples

    showClass("DEGs")

[Package tRanslatome version 1.18.5 Index]