miner

mechanistic inference of node-edge relationships

Command line documentation

https://baliga-lab.github.io/miner/

tutorial information

A template with instructions and code for performing a miner analysis is provided in the miner/src directory.

The template can be opened using Anaconda by selecting jupyter notebook from the user interface, or by simply typing "jupyter notebook" into the command line.

what you need to get started

Before the miner analysis can be performed, the gene expression data to be analyzed must be added to the miner/data directory with the filename "expressionData.csv". Ensure that your expression data is of the form log2(TPM+1) or log2(FPKM+1).

If survival analysis is desired, a survival file with the name "survival.csv" must added to the miner/data directory

If causal analysis is desired, a mutation file with the name "mutations.csv" must added to the miner/data directory

where to put your data

miner will search for specific filenames in the miner/data folder. In order to avoid "File does not exist" errors, do the following: 1. Name your expression data "expressionData.csv" 2. Name your mutation data "mutations.csv" (only for causal analysis) 3. Name your survival data "survival.csv" (only for survival analysis)

Note that the gene names will be converted to Ensembl Gene ID format

common mistakes to avoid

1. miner does not support expression data in counts format. Ensure that data is in log2(TPM+1) or log2(FPKM+1) format.
2. miner will look for gene names (ensembl, entrez, symbol, etc.) in the first column or first row of the expressionData.csv file. If the expression data does not have gene labels, an error will be returned. If you do not have gene names (e.g., your data is not gene expression), skip the "miner.identifierConversion(expressionData)" line in order to avoid errors.