Part of the Synthetic Lethality detection in Genomics toolkit. Detects bimodality and non-normality in all genes across the dataset. Compares all pairwise combinations of bimodal genes and searches for mutually exclusive low expression as evidence of potential synthetic lethality. Scores gene-pairs based on the presence of mutual exclusive bimodality and the distribution of signal intensity across the rest of the dataset.
BIGEE(
bisepData=data,
sampleType=c("cell_line", "cell_line_low", "patient", "patient_low")
)A matrix containing three columns. Columns 1 and 2 are the gene symbols that make up the candidate synthetic lethal gene pairs. Column 3 is the score calculated the tool to rank the statistical significance of the gene pairs.
This should be the output from the BISEP function.
The type of sample being analysed. Select 'cell_line' or 'patient' for datasets with greater than ~200 samples. For datasets with less than ~200 samples, use 'cell_line_low' or 'patient_low'.
Mark Wappett
Lower sample numbers have more stringent bimodality hurdles to clear in order to keep the false positive rate lower. The tool returns a percentage complete text window so the user can observe the status of the job.