# Analysis of co-knock-down RNAi data

## Documentation for package ‘coRNAi’ version 1.8.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

BetweenScreenPlot | reproducibility plots
BoxPlotShorth | Boxplot with horizontal bars at the midpoint of the shorth
cellHTS2df | converts cellHTS objects to dataframes
cortestmatrices | Function to extract correlations and corresponding p-values from interaction matrix.
data2graph | Function to create .dot files for graph representation of data
df2array | function to do go from data frame to an array with values
df2fitmatrix | matrix for lmFit from dataframe
df2lmFit | lmFit from dataframe
estmodel | Function to do estimate the main effects from data using median, mean or shorth.
faultyscreen | faulty screen
InteractGraph | functions to visualize interactions as a graph
interactiontable | Returns a list of interactions with associated statistics.
InteractLevelPlot | function to visualize interactions as a levelplot
key | A key to data set screen1, contains (additional) information about the genes in the screen.
lmmain | main effect estimation
MainFitPlot | Diagnostic plot
MAplot | plot variation vs signal intensity
PlotHeatmap | Plot a heatmap of interactions
Pplot | Function to plot cumulative p-values
repplots | reproducibility plots
rlmmain | main effect estimation
screen1_raw | screen1 raw data
screen2_raw | screen2 raw data
SDplot | plot variation vs signal intensity
signalplots | plot variation vs signal intensity
tt2matrix | Extracting data from a toptable and format it to matrix
updateDf | updates dataframe after fitting of main estimates
weightDf | Function to indicate which data points should be involved in down stream analysis.
WithinScreenPlot | reproducibility plots