JODA algorithm for quantifying gene deregulation using knowledge


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Documentation for package ‘joda’ version 1.14.0

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beliefs.damage Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
beliefs.healthy Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
data.damage Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
data.healthy Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
deregulation.p.values Calculating deregulation p-values using resampling method.
deregulation.scores Calculating deregulation scores.
differential.probs Calculating probabilities of differential expression in perturbation experiments
model.damage Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
model.healthy Knockout data for three regulators: ATM, RelA and p53 in two different cell populations: healthy (referred to as normal) cells and cells treated with neocarzinostatin (referred to as damaged cells).
regulation.scores Calculating regulation scores.