Analysis of co-knock-down RNAi data


[Up] [Top]

Documentation for package ‘coRNAi’ version 1.10.1

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