SDplot

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


The SD plot displays the standard deviations of the genes on the x-axis and the log2 fold changes on the y-axis. The upper plot represents a SD plot for the first level of gene expression analysis, whereas the other one refers to the second level. DEGs are color labeled. This function takes as input an object of class <code>DEGs</code>.


standard deviation

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.

SDplot: SDplotHelpfile

Description

Usage

Arguments

See Also

Examples