CRISPR Screen and Gene Expression Differential Analysis

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Documentation for package ‘CEDA’ version 1.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

alphaBeta	Calculating a significance score of a gene based on the corresponding sgRNAs' p-values of the gene.
calculateGeneLFC	Calculating gene-level log fold ratios
calculateGenePval	Calculating gene level p-values using modified robust rank aggregation (alpha-RRA method) on sgRNAs' p-values
densityPlot	2D density contour plot of gene log2 fold ratios against gene expression levels
EMFit	Fitting multi-component normal mixture models by R package mixtools
makeRhoNull	Generating the null distribution of the significance score of a gene.
mda231	CRISPR screen data of cell line MDA-MB-231.
medianNormalization	Median normalization of sgRNA counts
normalMM	Performing empirical Bayes modeling on limma results
permuteLimma	Modeling CRISPR data with a permutation test between conditions by R package limma
preparePlotData	Prepare data for density plot and ridge plot
ridgePlot	Density ridgeline plot of gene expression levels for different FDR groups.
runLimma	Modeling CRISPR screen data by R package limma
scatterPlot	Scatter plot of log2 fold ratios against gene expression levels