Scatterplot

object

a character string specifying if the plot is saved in jpeg (<code>jpeg</code>), postscript (<code>postscript</code>), pdf (<code>pdf</code>) format, or it is simply displayed on the screen(<code>on screen</code>). By default this value is <code>on screen</code>.

outputformat

a character vector of gene names that will be explicitly highlighted in the scatterplot, if they match any gene contained in the object of class <code>DEGs</code>. By default this vector is empty.

track


This plot shows each gene as dot uniquely determined by its log2 fold change at the first level (represented on the x-axis) and the fold change at the second level (represented on the y-axis).


scatterplot

Fold Change

DEGs

Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods:  Rank Product, Translational Efficiency, t-test, SAM, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.

Scatterplot: ScatterplotHelpfile

Description

Usage

Arguments

See Also

Examples