DEGs: Class 'DEGs'
In tRanslatome: Comparison between multiple levels of gene expression

Description Slots Accessors Methods Author(s) See Also Examples

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

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:

log2 FC(1st level), log2 fold change in the first level,
avg(1st level,control), average signal intensities of the control samples in the first level,
sd(1st level,control), standard deviation of the signal intensities of the control samples in the first level,
avg(1st level,treated), average signal intensities of the treated samples in the first level,
sd(1st level,treated), standard deviation of the signal intensities of the treated samples in the first level,
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),
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),
log2 FC(2nd level), log2 fold change in the second level,
avg(2nd level,control), average signal intensities of the control samples in the second level,
sd(2nd level,control), standard deviation of the signal intensities of the control samples in the second level,
avg(2nd level,treated), average signal intensities of the treated samples in the second level,
sd(2nd level,treated), standard deviation of the signal intensities of the treated samples in the second level,
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),
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),
level1Up, boolean value set to 1 if the gene is upregulated in the first level, otherwise set to 0,
level1Down, boolean value set to 1 if the gene is downregulated in the first level, otherwise set to 0,
level2Up, boolean value set to 1 if the gene is upregulated in the second level, otherwise set to 0,
level2Down, boolean value set to 1 if the gene is downregulated in the second level, otherwise set to 0,
DownDown, boolean value set to 1 if the gene is downregulated in both levels, otherwise set to 0,
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,
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,
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.

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.

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.