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coRNAi (version 1.22.0)

Analysis of co-knock-down RNAi data

Description

Analysis of combinatorial cell-based RNAi screens

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Version

Version

1.22.0

License

Artistic-2.0

Maintainer

Elin Axelsson

Last Published

February 15th, 2017

Functions in coRNAi (1.22.0)

InteractGraph

functions to visualize interactions as a graph
data2graph

Function to create .dot files for graph representation of data
key

A key to data set screen1, contains (additional) information about the genes in the screen.
screen1_raw

screen1 raw data
LS main

main effect estimation
weightDf

Function to indicate which data points should be involved in down stream analysis.
cortestmatrices

Function to extract correlations and corresponding p-values from interaction matrix.
updateDf

updates dataframe after fitting of main estimates
signalplots

plot variation vs signal intensity
PlotHeatmap

Plot a heatmap of interactions
df2fitmatrix

matrix for lmFit from dataframe
interactiontable

Returns a list of interactions with associated statistics.
estmodel

Function to do estimate the main effects from data using median, mean or shorth.
faultyscreen

faulty screen
InteractLevelPlot

function to visualize interactions as a levelplot
repplots

reproducibility plots
df2array

function to do go from data frame to an array with values
MainFitPlot

Diagnostic plot
Pplot

Function to plot cumulative p-values
df2lmFit

lmFit from dataframe
tt2matrix

Extracting data from a toptable and format it to matrix
screen2_raw

screen2 raw data
cellHTS2df

converts cellHTS objects to dataframes
BoxPlotShorth

Boxplot with horizontal bars at the midpoint of the shorth