| BIGEE {BiSEp} | R Documentation |
BIGEE: Bimodal Gene Expression Exclusivity.
Description
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.
Usage
BIGEE(
bisepData=data,
sampleType=c("cell_line", "cell_line_low", "patient", "patient_low")
)
Arguments
bisepData |
This should be the output from the BISEP function. |
sampleType |
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'. |
Details
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.
Value
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.
Author(s)
Mark Wappett