Report of DEG analysis


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Documentation for package ‘DEGreport’ version 1.30.3

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DEGreport-package Deprecated functions in package DEGreport
as.DEGSet DEGSet
as.DEGSet-method DEGSet
createReport Create report of RNAseq DEG anlaysis
deg Method to get all table stored for an specific comparison
deg-method Method to get all table stored for an specific comparison
degCheckFactors Distribution of gene ratios used to calculate Size Factors.
degColors Make nice colors for metadata
degComps Automatize the use of 'results()' for multiple comparisons
degCorCov Calculate the correlation relationshipt among all covariates in the metadata table
degCorrect Method to get the default table to use.
degCorrect-method Method to get the default table to use.
degCovariates Find correlation between pcs and covariates
degDefault Method to get the default table to use.
degDefault-method Method to get the default table to use.
degFilter Filter genes by group
degMA MA-plot from base means and log fold changes
degMB Distribution of expression of DE genes compared to the background
degMDS Plot MDS from normalized count data
degMean Distribution of pvalues by expression range
degMerge Integrate data comming from degPattern into one data object
degMV Correlation of the standard desviation and the mean of the abundance of a set of genes.
degObj Create a deg object that can be used to plot expression values at shiny server:runGist(9930881)
degPatterns Make groups of genes using expression profile.
degPCA smart PCA from count matrix data
degPlot Plot top genes allowing more variables to color and shape points
degPlotCluster Plot clusters from degPattern function output
degPlotWide Plot selected genes on a wide format
degQC Plot main figures showing p-values distribution and mean-variance correlation
DEGreport Deprecated functions in package DEGreport
degResults Complete report from DESeq2 analysis
DEGSet DEGSet
DEGSet-class DEGSet
degSignature Plot gene signature for each group and signature
degSummary Print Summary Statistics of Alpha Level Cutoffs
degVar Distribution of pvalues by standard desviation range
degVB Distribution of the standard desviation of DE genes compared to the background
degVolcano Create volcano plot from log2FC and adjusted pvalues data frame
geneInfo data.frame with chromose information for each gene
geom_cor Add correlation and p-value to a ggplot2 plot
humanGender DGEList object for DE genes betwen Male and Females
significants Method to get the significant genes
significants-method Method to get the significant genes