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Computational method to infer cancer-associated ceRNA interaction networks
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README.md

Cancerin

Cancerin is a tool to infer genome-wide cancer-associated ceRNA interaction network in cancer.

Scripts to run Cancerin are in run_cancerin.R. Required inputs for Cancerin include:

  • Four dataframes contains gene-level information of RNA and miRNA expression, copy number alteration, and DNA methylation. The corresponding variable names used in run_cancerin.R are RNA, miRNA, cna, and methyl.
    • Each column in those dataframes refer to a tumor sample.
    • Each row in the RNA, cna, and methyl refers to RNA expression level, copy number, and methylation beta value of a differenitally expressed (DE) RNAs, respectively. Each row in miRNA refers to the expression of a DE miRNA.
  • A dataframe named tf.target.interactions. Each row in tf.target.interactions refers to a putative interaction between a transcription factor (TF) and a gene.
  • A dataframe named miRNA.target.interactions. Each row in miRNA.target.interactions refers to a putative interaction between a miRNA and a gene.

Sample input data for Cancerin could be found in sampleData.rda.

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