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