Report of DEG analysis


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Documentation for package ‘DEGreport’ version 1.0.0

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createReport Create report of RNAseq DEG anlaysis
degBI Get the estimates of the fold change (FC) mean from a FC distribution using bayesian inference
degBIcmd Apply bayesian inference to estimate the average fold change (FC) of a distribution
degComb Get random combinations of two groups
degFC get the FC for each gene between two groups
degMB Distribution of expression of DE genes compared to the background
degMean Distribution of pvalues by expression range
degMV Correlation of the standard desviation and the mean of the abundance of a set of genes.
degNcomb Get number of potential combinations of two vectors
degObj Create a deg object that can be used to plot expression values at shiny server:runGist(9930881)
degPR plot the correlation between the rank according estimator and the rank according FC
degRank Get rank data frame with best score on the top
DEGreportSet list object for DE genes betwen Male and Females
degVar Distribution of pvalues by standard desviation range
degVB Distribution of the standard desviation of DE genes compared to the background
figurebyexp Wrap figure from 'degMB' into a Nozzle object
figurebyvar Wrap figure from 'degVB' into a Nozzle object
figurepvaluebyexp Wrap figure from 'degMean' into a Nozzle object
figurepvaluebyvar Wrap figure from 'degVar' into a Nozzle object
figurepvaluebyvarexp Wrap figure from 'degMV' into a Nozzle object
figurerank Wrap figure from 'plotrank' into a Nozzle object
geneInfo data.frame with chromose information for each gene
humanSexDEedgeR edgeR object for DE genes betwen Male and Females
tablerank Create table for Nozzle report